@molgenis/vip-report-template 8.2.2 → 8.3.0

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Files changed (17) hide show
  1. package/package.json +1 -1
  2. package/scripts/validateConfig/schema.ts +2 -0
  3. package/src/components/field/composed/FieldComposed.tsx +10 -0
  4. package/src/components/field/composed/FieldConfidenceInterval.tsx +14 -0
  5. package/src/components/field/composed/FieldGenotypeStr.tsx +3 -1
  6. package/src/components/field/composed/FieldSpanningReads.tsx +14 -0
  7. package/src/mocks/GRCh38/field_metadata.json +11 -13
  8. package/src/mocks/GRCh38/vcf/str.db.blob +0 -0
  9. package/src/mocks/GRCh38/vcf/str.vcf +179 -177
  10. package/src/mocks/config_cram.json +9 -4
  11. package/src/mocks/config_default_values.json +6 -2
  12. package/src/mocks/config_vcf.json +4 -4
  13. package/src/types/config.d.ts +2 -0
  14. package/src/types/configCellComposed.d.ts +14 -2
  15. package/src/utils/config/configCellsComposed.ts +89 -15
  16. package/src/utils/config/configValidator.precompiled.ts +80 -0
  17. package/tests/utils/config/configCellsComposed.test.ts +44 -32
package/src/mocks/GRCh38/vcf/str.vcf CHANGED
@@ -4,20 +4,17 @@
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  ##ASV_ACMG_class=AnnotSv 'ACMG_class' output.
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  ##ASV_AnnotSV_ranking_criteria=AnnotSv 'AnnotSV_ranking_criteria' output.
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  ##ASV_AnnotSV_ranking_score=AnnotSv 'AnnotSV_ranking_score' output.
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+ ##ASV_Gene_name=AnnotSv 'Gene_name' output.
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+ ##ASV_RE_gene=AnnotSv 'RE_gene' output.
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  ##CAPICE_CL=CAPICE classification
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  ##CAPICE_SC=CAPICE score
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- ##FATHMM_MKL_NC=FATHMM_MKL_NC: Predict the Functional Consequences of Non-Coding Single Nucleotide VariantsRedirect (SNVs)
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- ##FILTER=<ID=LowDepth,Description="The overall locus depth is below 10x or number of reads spanning one or both breakends is below 5">
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+ ##FATHMM_MKL_NC=FATHMM_MKL_NC: Predict the Functional Consequences of Non-Coding Single Nucleotide Variants (SNVs)
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  ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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- ##FORMAT=<ID=ADFL,Number=1,Type=String,Description="Number of flanking reads consistent with the allele">
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- ##FORMAT=<ID=ADIR,Number=1,Type=String,Description="Number of in-repeat reads consistent with the allele">
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- ##FORMAT=<ID=ADSP,Number=1,Type=String,Description="Number of spanning reads consistent with the allele">
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  ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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- ##FORMAT=<ID=LC,Number=1,Type=Float,Description="Locus coverage">
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- ##FORMAT=<ID=REPCI,Number=1,Type=String,Description="Confidence interval for REPCN">
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- ##FORMAT=<ID=REPCN,Number=1,Type=String,Description="Number of repeat units spanned by the allele">
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- ##FORMAT=<ID=SO,Number=1,Type=String,Description="Type of reads that support the allele; can be SPANNING, FLANKING, or INREPEAT meaning that the reads span, flank, or are fully contained in the repeat">
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+ ##FORMAT=<ID=LC,Number=1,Type=Integer,Description="Locus coverage">
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+ ##FORMAT=<ID=RU_SPAN,Number=A,Type=Integer,Description="Number of spanning reads per allele.">
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  ##FORMAT=<ID=VI,Number=.,Type=String,Description="An enumeration of possible inheritance modes based on the pedigree of the sample. Potential values: AD, AD_IP, AR, AR_C, XLR, XLD">
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+ ##FORMAT=<ID=VIAB,Number=1,Type=Float,Description="VIP calculated allele balance">
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  ##FORMAT=<ID=VIC,Number=1,Type=String,Description="Possible Compound hetrozygote variants.">
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  ##FORMAT=<ID=VID,Number=1,Type=Integer,Description="De novo variant.">
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  ##FORMAT=<ID=VIG,Number=.,Type=String,Description="Genes with a (potential) inheritance match.">
@@ -25,18 +22,20 @@
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  ##FORMAT=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
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  ##FORMAT=<ID=VIPP_S,Number=.,Type=String,Description="VIP decision tree path.">
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  ##Grantham=Grantham Matrix score - Grantham, R. Amino Acid Difference Formula to Help Explain Protein Evolution, Science 1974 Sep 6;185(4154):862-4.
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- ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|Grantham|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|existing_InFrame_oORFs|existing_OutOfFrame_oORFs|existing_uORFs|five_prime_UTR_variant_annotation|five_prime_UTR_variant_consequence|IncompletePenetrance|InheritanceModesGene|VKGL|VKGL_CL|gnomAD_AF|gnomAD_COV|gnomAD_FAF95|gnomAD_FAF99|gnomAD_HN|gnomAD_QC|gnomAD_SRC|clinVar_CLNID|clinVar_CLNREVSTAT|clinVar_CLNSIG|clinVar_CLNSIGINCL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|ALPHSCORE|ncER|FATHMM_MKL_NC|ReMM|phyloP|VIPC|VIPP">
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+ ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|Grantham|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|existing_InFrame_oORFs|existing_OutOfFrame_oORFs|existing_uORFs|five_prime_UTR_variant_annotation|five_prime_UTR_variant_consequence|IncompletePenetrance|InheritanceModesGene|VKGL|VKGL_CL|gnomAD_AF|gnomAD_COV|gnomAD_FAF95|gnomAD_FAF99|gnomAD_HN|gnomAD_QC|gnomAD_SRC|clinVar_CLNID|clinVar_CLNREVSTAT|clinVar_CLNSIG|clinVar_CLNSIGINCL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|ASV_Gene_name|ASV_RE_gene|ALPHSCORE|ncER|FATHMM_MKL_NC|ReMM|apogee_Score|apogee_Uscore|mitoTip_Quartile|mitoTip_Score|phyloP|VIPC|VIPP">
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  ##INFO=<ID=Disease,Number=1,Type=String,Description="Associated disorder">
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  ##INFO=<ID=DisplayRU,Number=1,Type=String,Description="Display repeat unit familiar to clinician">
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- ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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+ ##INFO=<ID=END,Number=1,Type=Integer,Description="End position">
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  ##INFO=<ID=HGNCId,Number=1,Type=Integer,Description="HGNC gene id for associated disease gene">
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  ##INFO=<ID=InheritanceMode,Number=1,Type=String,Description="Main mode of inheritance for disorder">
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  ##INFO=<ID=OLD_REC,Number=1,Type=String,Description="Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX">
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- ##INFO=<ID=REF,Number=1,Type=Integer,Description="Reference copy number">
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- ##INFO=<ID=REPID,Number=1,Type=String,Description="Repeat identifier as specified in the variant catalog">
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- ##INFO=<ID=RL,Number=1,Type=Integer,Description="Reference length in bp">
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- ##INFO=<ID=RU,Number=1,Type=String,Description="Repeat unit in the reference orientation">
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- ##INFO=<ID=RUMATCH,Number=0,Type=Flag,Description="Flag indicating if the called repeat unit matched the repeat unit in the loci bed file.">
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+ ##INFO=<ID=REPID,Number=1,Type=String,Description="Locus identifier.">
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+ ##INFO=<ID=RU_CALL,Number=1,Type=String,Description="Most frequent actual repeat motif">
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+ ##INFO=<ID=RU_CAT,Number=1,Type=String,Description="Catalog repeat motif">
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+ ##INFO=<ID=RU_CI,Number=A,Type=String,Description="95% confidence interval per allele. 'NA' if less than 2 reads were present.">
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+ ##INFO=<ID=RU_MATCH,Number=0,Type=Flag,Description="RU call matches catalog (allowing shift/IUPAC)">
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+ ##INFO=<ID=RU_NR,Number=A,Type=String,Description="Number of repeat units per allele.">
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+ ##INFO=<ID=RU_SEEN,Number=.,Type=String,Description="All RUs encountered with read counts">
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  ##INFO=<ID=RankScore,Number=1,Type=String,Description="RankScore for variant in this family as family(str):score(int)">
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  ##INFO=<ID=STR_NORMAL_MAX,Number=1,Type=Integer,Description="Max number of repeats allowed to call as normal">
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  ##INFO=<ID=STR_PATHOLOGIC_MIN,Number=1,Type=Integer,Description="Min number of repeats required to call as pathologic">
@@ -47,11 +46,10 @@
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  ##INFO=<ID=SourceId,Number=1,Type=String,Description="Source id for variant definition">
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  ##INFO=<ID=SweGenMean,Number=1,Type=Float,Description="Average number of repeat unit copies in population">
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  ##INFO=<ID=SweGenStd,Number=1,Type=Float,Description="Standard deviation of number of repeat unit copies in population">
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- ##INFO=<ID=VARID,Number=1,Type=String,Description="Variant identifier as specified in the variant catalog">
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  ##INFO=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification (samples).">
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  ##INFO=<ID=phyloP,Number=.,Type=String,Description="[PATH]/hg38.phyloP100way.bw">
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- ##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance, based on '<PATH>/vip/v7.9.0/resources/inheritance_20240115.tsv' .
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- ##InheritanceModesGene=List of inheritance modes for the gene, based on '<PATH>/vip/v7.9.0/resources/inheritance_20240115.tsv'
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+ ##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance, based on '<PATH>/inheritance_20250411.tsv' .
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+ ##InheritanceModesGene=List of inheritance modes for the gene, based on '<PATH>/inheritance_20250411.tsv'
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  ##ReMM=ReMM scores. The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding variations (SNVs and small InDels) in the human genome (hg19) in terms of Mendelian diseases.
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  ##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
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  ##SpliceAI_pred_DP_AL=SpliceAI predicted effect on splicing. Delta position for acceptor loss
@@ -62,45 +60,45 @@
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  ##SpliceAI_pred_DS_DG=SpliceAI predicted effect on splicing. Delta score for donor gain
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  ##SpliceAI_pred_DS_DL=SpliceAI predicted effect on splicing. Delta score for donor loss
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  ##SpliceAI_pred_SYMBOL=SpliceAI gene symbol
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- ##VEP-command-line='vep --allele_number --allow_non_variant --assembly GRCh38 --buffer_size 1000 --cache --compress_output bgzip --custom [PATH]/hg38.phyloP100way.bw,phyloP,bigwig,exact,0 --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/plugins --dont_skip --exclude_predicted --fasta [PATH]/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --flag_pick_allele --fork 4 --format vcf --hgvs --input_file preprocessed_stranger_<removed>_normalized.vcf.gz --no_stats --numbers --offline --output_file <removed>_annotated.vcf.gz --plugin [PATH]/GRCh38_ReMM.tsv.gz --polyphen s --pubmed --refseq --safe --shift_3prime --sift s --symbol --total_length --use_given_ref --vcf'
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- ##VEP="v111" time="2024-09-02 10:29:58" cache="<PATH>/vip/v7.9.0/resources/vep/cache/homo_sapiens_refseq/111_GRCh38" ensembl-variation=111.d616b1e ensembl-io=111.dbba8d6 ensembl-funcgen=111.5327cdd ensembl=111.a6cc543 1000genomes="phase3" COSMIC="98" ClinVar="202306" HGMD-PUBLIC="20204" assembly="GRCh38.p14" dbSNP="156" gencode="GENCODE 45" genebuild="2014-07" gnomADe="r2.1.1" gnomADg="v3.1.2" polyphen="2.2.3" refseq="GCF_000001405.40-RS_2023_03 - GCF_000001405.40_GRCh38.p14_genomic.gff" regbuild="1.0" sift="6.2.1"
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+ ##VEP-command-line='vep --allele_number --allow_non_variant --assembly GRCh38 --buffer_size 1000 --cache --compress_output bgzip --custom [PATH]/hg38.phyloP100way.bw,phyloP,bigwig,exact,0 --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/plugins --dont_skip --exclude_predicted --fasta [PATH]/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --flag_pick_allele --fork 4 --format vcf --hgvs --input_file preprocessed_stranger_vip_normalized.vcf.gz --no_stats --numbers --offline --output_file vep_vip_annotated.vcf.gz --plugin [PATH]/mitotip_scores_20251118.tsv.gz --polyphen s --pubmed --refseq --safe --shift_3prime --sift s --symbol --total_length --use_given_ref --vcf'
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+ ##VEP="v111" time="2026-01-29 09:15:08" cache="<PATH>/111_GRCh38" ensembl=111.a6cc543 ensembl-funcgen=111.5327cdd ensembl-io=111.dbba8d6 ensembl-variation=111.d616b1e 1000genomes="phase3" COSMIC="98" ClinVar="202306" HGMD-PUBLIC="20204" assembly="GRCh38.p14" dbSNP="156" gencode="GENCODE 45" genebuild="2014-07" gnomADe="r2.1.1" gnomADg="v3.1.2" polyphen="2.2.3" refseq="GCF_000001405.40-RS_2023_03 - GCF_000001405.40_GRCh38.p14_genomic.gff" regbuild="1.0" sift="6.2.1"
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  ##VIPC=VIP decision tree classification
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  ##VIPP=VIP decision tree path (ampersand separated)
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- ##VIP_treeCommand=--input <removed>_annotated.vcf.gz --metadata <PATH>/vip/v7.9.0/resources/field_metadata.json --config <PATH>/resources/VIP_tree_STR_v1.0.0.json --path --output <removed>_classified.vcf.gz
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- ##VIP_treeVersion=4.1.1
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- ##VKGL=file:<PATH>/vip/v7.9.0/resources/GRCh38/vkgl_consensus_20240401.tsv'
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+ ##VIP_treeCommand=--input vip_annotated.vcf.gz_replaced.vcf.gz --metadata <PATH>/field_metadata.json --config <PATH>/decision_tree_GRCh38.json --path --output vip_classified.vcf.gz_replaced.vcf.gz
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+ ##VIP_treeVersion=6.0.0
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+ ##VKGL=file:/groups/umcg-gcc/tmp02/projects/vipt/vip/data/resources/GRCh38/vkgl_consensus_20250401.tsv'
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  ##VKGL_CL=VKGL consensus variant classification.
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- ##bcftools_viewCommand=view --regions-file LX002_v1.0.0.bed --output-type z --output <removed>_bed_filtered.vcf.gz <removed>_fam0_<removed>_str.vcf.gz; Date=Mon Sep 2 10:29:26 2024
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- ##bcftools_viewVersion=1.17+htslib-1.17
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+ ##apogee_Score=Score assigned by APOGEE
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+ ##apogee_Uscore=Unbiased score assigned by APOGEE
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  ##clinVar_CLNID=ClinVar variation identifier
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  ##clinVar_CLNREVSTAT=ClinVar review status for the Variation ID
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  ##clinVar_CLNSIG=Clinical significance for this single variant; multiple values are separated by a vertical bar
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  ##clinVar_CLNSIGINCL=Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance; multiple values are separated by a vertical bar
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  ##contig=<ID=chr1,length=248956422>
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+ ##contig=<ID=chr2,length=242193529>
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+ ##contig=<ID=chr3,length=198295559>
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+ ##contig=<ID=chr4,length=190214555>
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+ ##contig=<ID=chr5,length=181538259>
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+ ##contig=<ID=chr6,length=170805979>
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+ ##contig=<ID=chr7,length=159345973>
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+ ##contig=<ID=chr8,length=145138636>
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+ ##contig=<ID=chr9,length=138394717>
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  ##contig=<ID=chr10,length=133797422>
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  ##contig=<ID=chr11,length=135086622>
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- ##contig=<ID=chr11_KI270721v1_random,length=100316>
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  ##contig=<ID=chr12,length=133275309>
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  ##contig=<ID=chr13,length=114364328>
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  ##contig=<ID=chr14,length=107043718>
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- ##contig=<ID=chr14_GL000009v2_random,length=201709>
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- ##contig=<ID=chr14_GL000194v1_random,length=191469>
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- ##contig=<ID=chr14_GL000225v1_random,length=211173>
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- ##contig=<ID=chr14_KI270722v1_random,length=194050>
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- ##contig=<ID=chr14_KI270723v1_random,length=38115>
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- ##contig=<ID=chr14_KI270724v1_random,length=39555>
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- ##contig=<ID=chr14_KI270725v1_random,length=172810>
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- ##contig=<ID=chr14_KI270726v1_random,length=43739>
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  ##contig=<ID=chr15,length=101991189>
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- ##contig=<ID=chr15_KI270727v1_random,length=448248>
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  ##contig=<ID=chr16,length=90338345>
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- ##contig=<ID=chr16_KI270728v1_random,length=1872759>
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  ##contig=<ID=chr17,length=83257441>
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- ##contig=<ID=chr17_GL000205v2_random,length=185591>
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- ##contig=<ID=chr17_KI270729v1_random,length=280839>
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- ##contig=<ID=chr17_KI270730v1_random,length=112551>
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  ##contig=<ID=chr18,length=80373285>
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  ##contig=<ID=chr19,length=58617616>
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+ ##contig=<ID=chr20,length=64444167>
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+ ##contig=<ID=chr21,length=46709983>
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+ ##contig=<ID=chr22,length=50818468>
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+ ##contig=<ID=chrX,length=156040895>
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+ ##contig=<ID=chrY,length=57227415>
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+ ##contig=<ID=chrM,length=16569>
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  ##contig=<ID=chr1_KI270706v1_random,length=175055>
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  ##contig=<ID=chr1_KI270707v1_random,length=32032>
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  ##contig=<ID=chr1_KI270708v1_random,length=127682>
@@ -110,149 +108,147 @@
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  ##contig=<ID=chr1_KI270712v1_random,length=176043>
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  ##contig=<ID=chr1_KI270713v1_random,length=40745>
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  ##contig=<ID=chr1_KI270714v1_random,length=41717>
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- ##contig=<ID=chr2,length=242193529>
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- ##contig=<ID=chr20,length=64444167>
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- ##contig=<ID=chr21,length=46709983>
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- ##contig=<ID=chr22,length=50818468>
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- ##contig=<ID=chr22_KI270731v1_random,length=150754>
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- ##contig=<ID=chr22_KI270732v1_random,length=41543>
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- ##contig=<ID=chr22_KI270733v1_random,length=179772>
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- ##contig=<ID=chr22_KI270734v1_random,length=165050>
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- ##contig=<ID=chr22_KI270735v1_random,length=42811>
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- ##contig=<ID=chr22_KI270736v1_random,length=181920>
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- ##contig=<ID=chr22_KI270737v1_random,length=103838>
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- ##contig=<ID=chr22_KI270738v1_random,length=99375>
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- ##contig=<ID=chr22_KI270739v1_random,length=73985>
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  ##contig=<ID=chr2_KI270715v1_random,length=161471>
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  ##contig=<ID=chr2_KI270716v1_random,length=153799>
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- ##contig=<ID=chr3,length=198295559>
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  ##contig=<ID=chr3_GL000221v1_random,length=155397>
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- ##contig=<ID=chr4,length=190214555>
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  ##contig=<ID=chr4_GL000008v2_random,length=209709>
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- ##contig=<ID=chr5,length=181538259>
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  ##contig=<ID=chr5_GL000208v1_random,length=92689>
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- ##contig=<ID=chr6,length=170805979>
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- ##contig=<ID=chr7,length=159345973>
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- ##contig=<ID=chr8,length=145138636>
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- ##contig=<ID=chr9,length=138394717>
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  ##contig=<ID=chr9_KI270717v1_random,length=40062>
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  ##contig=<ID=chr9_KI270718v1_random,length=38054>
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  ##contig=<ID=chr9_KI270719v1_random,length=176845>
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  ##contig=<ID=chr9_KI270720v1_random,length=39050>
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- ##contig=<ID=chrEBV,length=171823>
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- ##contig=<ID=chrM,length=16569>
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- ##contig=<ID=chrUn_GL000195v1,length=182896>
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- ##contig=<ID=chrUn_GL000213v1,length=164239>
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- ##contig=<ID=chrUn_GL000214v1,length=137718>
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- ##contig=<ID=chrUn_GL000216v2,length=176608>
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- ##contig=<ID=chrUn_GL000218v1,length=161147>
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- ##contig=<ID=chrUn_GL000219v1,length=179198>
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- ##contig=<ID=chrUn_GL000220v1,length=161802>
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- ##contig=<ID=chrUn_GL000224v1,length=179693>
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- ##contig=<ID=chrUn_GL000226v1,length=15008>
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+ ##contig=<ID=chr11_KI270721v1_random,length=100316>
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+ ##contig=<ID=chr14_GL000009v2_random,length=201709>
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+ ##contig=<ID=chr14_GL000225v1_random,length=211173>
123
+ ##contig=<ID=chr14_KI270722v1_random,length=194050>
124
+ ##contig=<ID=chr14_GL000194v1_random,length=191469>
125
+ ##contig=<ID=chr14_KI270723v1_random,length=38115>
126
+ ##contig=<ID=chr14_KI270724v1_random,length=39555>
127
+ ##contig=<ID=chr14_KI270725v1_random,length=172810>
128
+ ##contig=<ID=chr14_KI270726v1_random,length=43739>
129
+ ##contig=<ID=chr15_KI270727v1_random,length=448248>
130
+ ##contig=<ID=chr16_KI270728v1_random,length=1872759>
131
+ ##contig=<ID=chr17_GL000205v2_random,length=185591>
132
+ ##contig=<ID=chr17_KI270729v1_random,length=280839>
133
+ ##contig=<ID=chr17_KI270730v1_random,length=112551>
134
+ ##contig=<ID=chr22_KI270731v1_random,length=150754>
135
+ ##contig=<ID=chr22_KI270732v1_random,length=41543>
136
+ ##contig=<ID=chr22_KI270733v1_random,length=179772>
137
+ ##contig=<ID=chr22_KI270734v1_random,length=165050>
138
+ ##contig=<ID=chr22_KI270735v1_random,length=42811>
139
+ ##contig=<ID=chr22_KI270736v1_random,length=181920>
140
+ ##contig=<ID=chr22_KI270737v1_random,length=103838>
141
+ ##contig=<ID=chr22_KI270738v1_random,length=99375>
142
+ ##contig=<ID=chr22_KI270739v1_random,length=73985>
143
+ ##contig=<ID=chrY_KI270740v1_random,length=37240>
153
144
  ##contig=<ID=chrUn_KI270302v1,length=2274>
154
- ##contig=<ID=chrUn_KI270303v1,length=1942>
155
145
  ##contig=<ID=chrUn_KI270304v1,length=2165>
146
+ ##contig=<ID=chrUn_KI270303v1,length=1942>
156
147
  ##contig=<ID=chrUn_KI270305v1,length=1472>
148
+ ##contig=<ID=chrUn_KI270322v1,length=21476>
149
+ ##contig=<ID=chrUn_KI270320v1,length=4416>
157
150
  ##contig=<ID=chrUn_KI270310v1,length=1201>
158
- ##contig=<ID=chrUn_KI270311v1,length=12399>
159
- ##contig=<ID=chrUn_KI270312v1,length=998>
160
- ##contig=<ID=chrUn_KI270315v1,length=2276>
161
151
  ##contig=<ID=chrUn_KI270316v1,length=1444>
152
+ ##contig=<ID=chrUn_KI270315v1,length=2276>
153
+ ##contig=<ID=chrUn_KI270312v1,length=998>
154
+ ##contig=<ID=chrUn_KI270311v1,length=12399>
162
155
  ##contig=<ID=chrUn_KI270317v1,length=37690>
163
- ##contig=<ID=chrUn_KI270320v1,length=4416>
164
- ##contig=<ID=chrUn_KI270322v1,length=21476>
165
- ##contig=<ID=chrUn_KI270329v1,length=1040>
166
- ##contig=<ID=chrUn_KI270330v1,length=1652>
167
- ##contig=<ID=chrUn_KI270333v1,length=2699>
168
- ##contig=<ID=chrUn_KI270334v1,length=1368>
169
- ##contig=<ID=chrUn_KI270335v1,length=1048>
170
- ##contig=<ID=chrUn_KI270336v1,length=1026>
171
- ##contig=<ID=chrUn_KI270337v1,length=1121>
172
- ##contig=<ID=chrUn_KI270338v1,length=1428>
173
- ##contig=<ID=chrUn_KI270340v1,length=1428>
174
- ##contig=<ID=chrUn_KI270362v1,length=3530>
175
- ##contig=<ID=chrUn_KI270363v1,length=1803>
176
- ##contig=<ID=chrUn_KI270364v1,length=2855>
177
- ##contig=<ID=chrUn_KI270366v1,length=8320>
178
- ##contig=<ID=chrUn_KI270371v1,length=2805>
179
- ##contig=<ID=chrUn_KI270372v1,length=1650>
180
- ##contig=<ID=chrUn_KI270373v1,length=1451>
181
- ##contig=<ID=chrUn_KI270374v1,length=2656>
182
- ##contig=<ID=chrUn_KI270375v1,length=2378>
183
- ##contig=<ID=chrUn_KI270376v1,length=1136>
184
- ##contig=<ID=chrUn_KI270378v1,length=1048>
185
- ##contig=<ID=chrUn_KI270379v1,length=1045>
186
- ##contig=<ID=chrUn_KI270381v1,length=1930>
187
- ##contig=<ID=chrUn_KI270382v1,length=4215>
188
- ##contig=<ID=chrUn_KI270383v1,length=1750>
189
- ##contig=<ID=chrUn_KI270384v1,length=1658>
190
- ##contig=<ID=chrUn_KI270385v1,length=990>
191
- ##contig=<ID=chrUn_KI270386v1,length=1788>
192
- ##contig=<ID=chrUn_KI270387v1,length=1537>
193
- ##contig=<ID=chrUn_KI270388v1,length=1216>
194
- ##contig=<ID=chrUn_KI270389v1,length=1298>
195
- ##contig=<ID=chrUn_KI270390v1,length=2387>
196
- ##contig=<ID=chrUn_KI270391v1,length=1484>
197
- ##contig=<ID=chrUn_KI270392v1,length=971>
198
- ##contig=<ID=chrUn_KI270393v1,length=1308>
199
- ##contig=<ID=chrUn_KI270394v1,length=970>
200
- ##contig=<ID=chrUn_KI270395v1,length=1143>
201
- ##contig=<ID=chrUn_KI270396v1,length=1880>
202
- ##contig=<ID=chrUn_KI270411v1,length=2646>
203
156
  ##contig=<ID=chrUn_KI270412v1,length=1179>
157
+ ##contig=<ID=chrUn_KI270411v1,length=2646>
204
158
  ##contig=<ID=chrUn_KI270414v1,length=2489>
205
- ##contig=<ID=chrUn_KI270417v1,length=2043>
206
- ##contig=<ID=chrUn_KI270418v1,length=2145>
207
159
  ##contig=<ID=chrUn_KI270419v1,length=1029>
160
+ ##contig=<ID=chrUn_KI270418v1,length=2145>
208
161
  ##contig=<ID=chrUn_KI270420v1,length=2321>
162
+ ##contig=<ID=chrUn_KI270424v1,length=2140>
163
+ ##contig=<ID=chrUn_KI270417v1,length=2043>
209
164
  ##contig=<ID=chrUn_KI270422v1,length=1445>
210
165
  ##contig=<ID=chrUn_KI270423v1,length=981>
211
- ##contig=<ID=chrUn_KI270424v1,length=2140>
212
166
  ##contig=<ID=chrUn_KI270425v1,length=1884>
213
167
  ##contig=<ID=chrUn_KI270429v1,length=1361>
214
- ##contig=<ID=chrUn_KI270435v1,length=92983>
215
- ##contig=<ID=chrUn_KI270438v1,length=112505>
216
168
  ##contig=<ID=chrUn_KI270442v1,length=392061>
217
- ##contig=<ID=chrUn_KI270448v1,length=7992>
218
- ##contig=<ID=chrUn_KI270465v1,length=1774>
219
169
  ##contig=<ID=chrUn_KI270466v1,length=1233>
170
+ ##contig=<ID=chrUn_KI270465v1,length=1774>
220
171
  ##contig=<ID=chrUn_KI270467v1,length=3920>
172
+ ##contig=<ID=chrUn_KI270435v1,length=92983>
173
+ ##contig=<ID=chrUn_KI270438v1,length=112505>
221
174
  ##contig=<ID=chrUn_KI270468v1,length=4055>
222
- ##contig=<ID=chrUn_KI270507v1,length=5353>
223
- ##contig=<ID=chrUn_KI270508v1,length=1951>
224
- ##contig=<ID=chrUn_KI270509v1,length=2318>
225
175
  ##contig=<ID=chrUn_KI270510v1,length=2415>
226
- ##contig=<ID=chrUn_KI270511v1,length=8127>
227
- ##contig=<ID=chrUn_KI270512v1,length=22689>
228
- ##contig=<ID=chrUn_KI270515v1,length=6361>
229
- ##contig=<ID=chrUn_KI270516v1,length=1300>
230
- ##contig=<ID=chrUn_KI270517v1,length=3253>
176
+ ##contig=<ID=chrUn_KI270509v1,length=2318>
231
177
  ##contig=<ID=chrUn_KI270518v1,length=2186>
178
+ ##contig=<ID=chrUn_KI270508v1,length=1951>
179
+ ##contig=<ID=chrUn_KI270516v1,length=1300>
180
+ ##contig=<ID=chrUn_KI270512v1,length=22689>
232
181
  ##contig=<ID=chrUn_KI270519v1,length=138126>
233
- ##contig=<ID=chrUn_KI270521v1,length=7642>
234
182
  ##contig=<ID=chrUn_KI270522v1,length=5674>
235
- ##contig=<ID=chrUn_KI270528v1,length=2983>
183
+ ##contig=<ID=chrUn_KI270511v1,length=8127>
184
+ ##contig=<ID=chrUn_KI270515v1,length=6361>
185
+ ##contig=<ID=chrUn_KI270507v1,length=5353>
186
+ ##contig=<ID=chrUn_KI270517v1,length=3253>
236
187
  ##contig=<ID=chrUn_KI270529v1,length=1899>
188
+ ##contig=<ID=chrUn_KI270528v1,length=2983>
237
189
  ##contig=<ID=chrUn_KI270530v1,length=2168>
238
- ##contig=<ID=chrUn_KI270538v1,length=91309>
239
190
  ##contig=<ID=chrUn_KI270539v1,length=993>
191
+ ##contig=<ID=chrUn_KI270538v1,length=91309>
240
192
  ##contig=<ID=chrUn_KI270544v1,length=1202>
241
193
  ##contig=<ID=chrUn_KI270548v1,length=1599>
242
- ##contig=<ID=chrUn_KI270579v1,length=31033>
243
- ##contig=<ID=chrUn_KI270580v1,length=1553>
244
- ##contig=<ID=chrUn_KI270581v1,length=7046>
245
- ##contig=<ID=chrUn_KI270582v1,length=6504>
246
194
  ##contig=<ID=chrUn_KI270583v1,length=1400>
247
- ##contig=<ID=chrUn_KI270584v1,length=4513>
248
195
  ##contig=<ID=chrUn_KI270587v1,length=2969>
249
- ##contig=<ID=chrUn_KI270588v1,length=6158>
196
+ ##contig=<ID=chrUn_KI270580v1,length=1553>
197
+ ##contig=<ID=chrUn_KI270581v1,length=7046>
198
+ ##contig=<ID=chrUn_KI270579v1,length=31033>
250
199
  ##contig=<ID=chrUn_KI270589v1,length=44474>
251
200
  ##contig=<ID=chrUn_KI270590v1,length=4685>
252
- ##contig=<ID=chrUn_KI270591v1,length=5796>
201
+ ##contig=<ID=chrUn_KI270584v1,length=4513>
202
+ ##contig=<ID=chrUn_KI270582v1,length=6504>
203
+ ##contig=<ID=chrUn_KI270588v1,length=6158>
253
204
  ##contig=<ID=chrUn_KI270593v1,length=3041>
205
+ ##contig=<ID=chrUn_KI270591v1,length=5796>
206
+ ##contig=<ID=chrUn_KI270330v1,length=1652>
207
+ ##contig=<ID=chrUn_KI270329v1,length=1040>
208
+ ##contig=<ID=chrUn_KI270334v1,length=1368>
209
+ ##contig=<ID=chrUn_KI270333v1,length=2699>
210
+ ##contig=<ID=chrUn_KI270335v1,length=1048>
211
+ ##contig=<ID=chrUn_KI270338v1,length=1428>
212
+ ##contig=<ID=chrUn_KI270340v1,length=1428>
213
+ ##contig=<ID=chrUn_KI270336v1,length=1026>
214
+ ##contig=<ID=chrUn_KI270337v1,length=1121>
215
+ ##contig=<ID=chrUn_KI270363v1,length=1803>
216
+ ##contig=<ID=chrUn_KI270364v1,length=2855>
217
+ ##contig=<ID=chrUn_KI270362v1,length=3530>
218
+ ##contig=<ID=chrUn_KI270366v1,length=8320>
219
+ ##contig=<ID=chrUn_KI270378v1,length=1048>
220
+ ##contig=<ID=chrUn_KI270379v1,length=1045>
221
+ ##contig=<ID=chrUn_KI270389v1,length=1298>
222
+ ##contig=<ID=chrUn_KI270390v1,length=2387>
223
+ ##contig=<ID=chrUn_KI270387v1,length=1537>
224
+ ##contig=<ID=chrUn_KI270395v1,length=1143>
225
+ ##contig=<ID=chrUn_KI270396v1,length=1880>
226
+ ##contig=<ID=chrUn_KI270388v1,length=1216>
227
+ ##contig=<ID=chrUn_KI270394v1,length=970>
228
+ ##contig=<ID=chrUn_KI270386v1,length=1788>
229
+ ##contig=<ID=chrUn_KI270391v1,length=1484>
230
+ ##contig=<ID=chrUn_KI270383v1,length=1750>
231
+ ##contig=<ID=chrUn_KI270393v1,length=1308>
232
+ ##contig=<ID=chrUn_KI270384v1,length=1658>
233
+ ##contig=<ID=chrUn_KI270392v1,length=971>
234
+ ##contig=<ID=chrUn_KI270381v1,length=1930>
235
+ ##contig=<ID=chrUn_KI270385v1,length=990>
236
+ ##contig=<ID=chrUn_KI270382v1,length=4215>
237
+ ##contig=<ID=chrUn_KI270376v1,length=1136>
238
+ ##contig=<ID=chrUn_KI270374v1,length=2656>
239
+ ##contig=<ID=chrUn_KI270372v1,length=1650>
240
+ ##contig=<ID=chrUn_KI270373v1,length=1451>
241
+ ##contig=<ID=chrUn_KI270375v1,length=2378>
242
+ ##contig=<ID=chrUn_KI270371v1,length=2805>
243
+ ##contig=<ID=chrUn_KI270448v1,length=7992>
244
+ ##contig=<ID=chrUn_KI270521v1,length=7642>
245
+ ##contig=<ID=chrUn_GL000195v1,length=182896>
246
+ ##contig=<ID=chrUn_GL000219v1,length=179198>
247
+ ##contig=<ID=chrUn_GL000220v1,length=161802>
248
+ ##contig=<ID=chrUn_GL000224v1,length=179693>
254
249
  ##contig=<ID=chrUn_KI270741v1,length=157432>
255
- ##contig=<ID=chrUn_KI270742v1,length=186739>
250
+ ##contig=<ID=chrUn_GL000226v1,length=15008>
251
+ ##contig=<ID=chrUn_GL000213v1,length=164239>
256
252
  ##contig=<ID=chrUn_KI270743v1,length=210658>
257
253
  ##contig=<ID=chrUn_KI270744v1,length=168472>
258
254
  ##contig=<ID=chrUn_KI270745v1,length=41891>
@@ -268,9 +264,11 @@
268
264
  ##contig=<ID=chrUn_KI270755v1,length=36723>
269
265
  ##contig=<ID=chrUn_KI270756v1,length=79590>
270
266
  ##contig=<ID=chrUn_KI270757v1,length=71251>
271
- ##contig=<ID=chrX,length=156040895>
272
- ##contig=<ID=chrY,length=57227415>
273
- ##contig=<ID=chrY_KI270740v1_random,length=37240>
267
+ ##contig=<ID=chrUn_GL000214v1,length=137718>
268
+ ##contig=<ID=chrUn_KI270742v1,length=186739>
269
+ ##contig=<ID=chrUn_GL000216v2,length=176608>
270
+ ##contig=<ID=chrUn_GL000218v1,length=161147>
271
+ ##contig=<ID=chrEBV,length=171823>
274
272
  ##existing_InFrame_oORFs=The number of existing inFrame overlapping ORFs (inFrame oORF) at the 5 prime UTR
275
273
  ##existing_OutOfFrame_oORFs=The number of existing out-of-frame overlapping ORFs (OutOfFrame oORF) at the 5 prime UTR
276
274
  ##existing_uORFs=The number of existing uORFs with a stop codon within the 5 prime UTR
@@ -283,39 +281,43 @@
283
281
  ##gnomAD_HN=gnomAD number of homozygotes
284
282
  ##gnomAD_QC=gnomAD quality control filters that failed
285
283
  ##gnomAD_SRC=gnomAD source: E=exomes, G=genomes, T=total
284
+ ##mitoTip_Quartile=MitoTip Quartile
285
+ ##mitoTip_Score=MitoTip Score
286
286
  ##ncER=ncER (https://www.nature.com/articles/s41467-019-13212-3) scores. This indicates the likelyhood of a location being essential in terms of regulation.
287
- ##reference=file://<PATH>/vip/v7.9.0/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant">
288
- ##source=strglr_1.4.4
289
287
  ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance">
290
- ##VIP_Version=7.9.0
291
- ##VIP_Command=nextflow -C <PATH>/vip/v7.9.0/config/nxf_fastq.config,<PATH>/resources/run_v1.0.0.cfg -log <PATH>/<removed>/run01/results/.nxf.log run <PATH>/vip/v7.9.0/vip_fastq.nf -offline -profile slurm -with-report <PATH>/<removed>/run01/results/nxf_report.html -with-timeline <PATH>/<removed>/run01/results/nxf_timeline.html --input <PATH>/<removed>/run01/vip/sample_sheet.tsv --output <PATH>/<removed>/run01/results
288
+ ##VIP_Version=8.4.5
289
+ ##VIP_Command=<PATH>/nextflow-24.10.6-dist -C <PATH>/nxf_cram.config,<PATH>/resources/nanopore_duo.cfg -log <PATH>/cram/nanopore_duo/.nxf.log run /<PATH>/vip_cram.nf -offline -profile slurm -with-report <PATH>/nxf_report.html -with-timeline <PATH>/nxf_timeline.html --input <PATH>/samplesheet.tsv --output <PATH>/nanopore_duo -resume
292
290
  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient
293
- chr1 149390803 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|NOTCH2NLC|100996717|Transcript|NM_001364013.2|protein_coding|1/5||||184-221/8729|17-54/882|6-18/293||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=NIID/OPDM3;DisplayRU=CGG;END=149390841;HGNCId=53924;REF=13;REPID=NOTCH2NLC;RL=39;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=60;STR_PATHOLOGIC_MIN=61;STR_STATUS=normal,normal;SVTYPE=STR;VARID=NOTCH2NLC;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:14/28:34:18-18/7-17:18/13:SPANNING/SPANNING:AR,AD::.:100996717:1:U1:gt&gq&only_IP&vim&exit_u1
294
- chr12 6936717 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATN1|1822|Transcript|NM_001940.4|protein_coding|5/10||||2039-2094/4702|1451-1506/3573|484-502/1190||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=DRPLA;DisplayRU=CAG;END=6936773;HGNCId=3033;REF=19;REPID=ATN1;RL=57;RU=CAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=35;STR_PATHOLOGIC_MIN=48;STR_STATUS=normal,normal;SVTYPE=STR;VARID=ATN1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:27/8:38:19-20/15-18:SPANNING/SPANNING:AR,AD::.:1822:1:U1:gt&gq&only_IP&vim&exit_u1
295
- chr12 111598950 . G <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN2|6311|Transcript|NM_001372574.1|protein_coding|1/25||||298-365/4347|17-84/3468|6-28/1155||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA2;DisplayRU=CTG;END=111599018;HGNCId=10555;REF=23;REPID=ATXN2;RL=69;RU=GCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=31;STR_PATHOLOGIC_MIN=32;STR_STATUS=normal;SVTYPE=STR;VARID=ATXN2;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:16.0/16.0:32:21-23/21-23:22/22:SPANNING/SPANNING:AR,AD::.:6311:1:U1:gt&gq&only_IP&vim&exit_u1
296
- chr13 70139384 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN8OS|6315|Transcript|NR_002717.2|antisense_RNA|5/5||||1104-1147/1472||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=70139428;REF=15;REPID=ATXN8;RL=45;RU=CTG;RUMATCH;SVTYPE=STR;VARID=ATXN8;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:21.5/21.5:45:15-16/15-16:16/16:SPANNING/SPANNING:AR,AD::.:6315:1:U1:gt&gq&only_IP&vim&exit_u1
297
- chr13 102161577 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|FGF14|2259|Transcript|NM_175929.3|protein_coding||1/4|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA27B;DisplayRU=GAA;END=102161726;HGNCId=3671;REF=50;REPID=FGF14;RL=150;RU=AAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=249;STR_PATHOLOGIC_MIN=250;STR_STATUS=normal,normal;SVTYPE=STR;VARID=FGF14;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:13/19:34:15-17/9-11:16/10:SPANNING/SPANNING:AR,AD::.:2259:1:U1:gt&gq&only_IP&vim&exit_u1
298
- chr14 92071010 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_004993.6|protein_coding|10/11||||914-945/6884|884-915/1086|295-305/361||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA3;DisplayRU=CTG;END=92071042;HGNCId=7106;REF=11;REPID=ATXN3;RL=33;RU=CTG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=44;STR_PATHOLOGIC_MIN=55;STR_STATUS=normal;SVTYPE=STR;VARID=ATXN3;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:18.0/18.0:39:19-21/19-21:20/20:SPANNING/SPANNING:AR,AD::.:4287:1:U1:gt&gq&only_IP&vim&exit_u1
299
- chr16 17470909 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|XYLT1|64131|Transcript|NM_022166.4|protein_coding|1/12||||40-51/9970||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&exit_vus;Disease=BSS;DisplayRU=GCC;END=17470921;HGNCId=15516;REF=1;REPID=XYLT1;RL=13;RU=GCCGCCGCC;RankScore=1:20;STR_NORMAL_MAX=20;STR_PATHOLOGIC_MIN=120;STR_STATUS=pre_mutation,normal;SVTYPE=STR;VARID=XYLT1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:12/13:33:22-23/16-20:22/18:SPANNING/SPANNING:AR,AD::.:64131:1:U1:gt&gq&only_IP&vim&exit_u1
300
- chr16 87604288 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|JPH3|57338|Transcript|NM_020655.4|protein_coding||1/4|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=HDL2;DisplayRU=CTG;END=87604329;HGNCId=14203;REF=14;REPID=JPH3;RL=42;RU=GCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=28;STR_PATHOLOGIC_MIN=41;STR_STATUS=normal;SVTYPE=STR;VARID=JPH3;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:20.5/20.5:44:15-16/15-16:16/16:SPANNING/SPANNING:AR,AD::.:57338:1:U1:gt&gq&only_IP&vim&exit_u1
301
- chr18 55586156 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001083962.2|protein_coding||2/19|||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=FECD;DisplayRU=GCA;END=55586227;HGNCId=11634;REF=24;REPID=TCF4;RL=72;RU=AGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=31;STR_PATHOLOGIC_MIN=50;STR_STATUS=normal,normal;SVTYPE=STR;VARID=TCF4;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:25/22:51:26-28/16-18:27/17:SPANNING/SPANNING:AR,AD::.:6925:1:U1:gt&gq&only_IP&vim&exit_u1
302
- chr19 13207859 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|CACNA1A|773|Transcript|NM_001127222.2|protein_coding|47/47||||7192-7229/8647|6937-6974/7521|2313-2325/2506||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA6;DisplayRU=CTG;END=13207897;HGNCId=1388;REF=13;REPID=CACNA1A;RL=39;RU=CTG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=18;STR_PATHOLOGIC_MIN=20;STR_STATUS=normal,normal;SVTYPE=STR;VARID=CACNA1A;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:33/2:39:11-12/6-8:11/7:SPANNING/SPANNING:AR,AD::.:773:1:U1:gt&gq&only_IP&vim&exit_u1
303
- chr19 14496043 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_005716.4|protein_coding|1/9||||54-84/1921||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&exit_vus;Disease=OPDM2;DisplayRU=CCG;END=14496074;HGNCId=1226;REF=5;REPID=GIPC1;RL=32;RU=CTCCGC;RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=97;STR_STATUS=normal,normal;SVTYPE=STR;VARID=GIPC1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:8/27:40:7-8/5-6:7/6:SPANNING/SPANNING:AR,AD::.:10755:1:U1:gt&gq&only_IP&vim&exit_u1
304
- chr19 45770205 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_004409.5|protein_coding|15/15||||2252-2310/2799||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD&AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=DM1;DisplayRU=CAG;END=45770264;HGNCId=2933;REF=20;REPID=DMPK;RL=60;RU=CAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=37;STR_PATHOLOGIC_MIN=50;STR_STATUS=normal,normal;SVTYPE=STR;VARID=DMPK;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:30/16:48:13-14/6-6:14/6:SPANNING/SPANNING:AR,AD::.:1760:1:U1:gt&gq&only_IP&vim&exit_u1
305
- chr2 176093060 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|HOXD13|3239|Transcript|NM_000523.4|protein_coding|1/2||||341-383/2416|171-213/1032|57-71/343||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD&AR||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;Disease=SPD1;DisplayRU=GCG;END=176093103;HGNCId=5136;REF=14;REPID=HOXD13;RL=44;RU=CGG;RUMATCH;RankScore=1:20;STR_NORMAL_MAX=15;STR_PATHOLOGIC_MIN=24;STR_STATUS=pre_mutation;SVTYPE=STR;VARID=HOXD13;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:21.5/21.5:45:15-16/15-16:16/16:SPANNING/SPANNING:AR,AD::.:3239:1:U1:gt&gq&only_IP&vim&exit_u1
306
- chr2 190880873 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GLS|2744|Transcript|NM_014905.5|protein_coding|1/18||||54-100/4840||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=GDPAG;DisplayRU=GCA;END=190880920;HGNCId=4331;REF=16;REPID=GLS;RL=48;RU=GCA;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=16;STR_PATHOLOGIC_MIN=680;STR_STATUS=normal,normal;SVTYPE=STR;VARID=GLS;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:36/2:42:12-14/7-8:13/7:SPANNING/SPANNING:AR,AD::.:2744:1:U1:gt&gq&only_IP&vim&exit_u1
307
- chr20 2652734 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|NOP56|10528|Transcript|NM_006392.4|protein_coding||1/11|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA36;DisplayRU=GGCCTG;END=2652757;HGNCId=15911;REF=4;REPID=NOP56;RL=24;RU=GGGCCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=14;STR_PATHOLOGIC_MIN=650;STR_STATUS=normal,normal;SVTYPE=STR;VARID=NOP56;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:23/2:27:7-8/5-5:7/5:SPANNING/SPANNING:AR,AD::.:10528:1:U1:gt&gq&only_IP&vim&exit_u1
308
- chr22 45795355 . A <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN10|25814|Transcript|NM_013236.4|protein_coding||9/11|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA10;DisplayRU=ATTCT;END=45795424;HGNCId=10549;REF=14;REPID=ATXN10;RL=70;RU=ATTCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=280;STR_STATUS=normal,normal;SVTYPE=STR;VARID=ATXN10;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:16/20:42:16-16/13-13:16/13:SPANNING/SPANNING:AR,AD::.:25814:1:U1:gt&gq&only_IP&vim&exit_u1
309
- chr3 63912686 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_001377405.1|protein_coding|3/13||||491-519/7076|89-117/2679|30-39/892||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA7;DisplayRU=CAG;END=63912715;HGNCId=10560;REF=10;REPID=ATXN7;RL=30;RU=GCA;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=19;STR_PATHOLOGIC_MIN=36;STR_STATUS=normal;SVTYPE=STR;VARID=ATXN7;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:14.5/14.5:31:9-12/9-12:11/11:SPANNING/SPANNING:AR,AD::.:6314:1:U1:gt&gq&only_IP&vim&exit_u1
310
- chr3 129172577 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_003418.5|protein_coding||1/4|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&exit_vus;Disease=DM2;DisplayRU=CAGG;END=129172656;HGNCId=13164;REF=10;REPID=CNBP;RL=80;RU=CAGACAGG;RankScore=1:10;STR_NORMAL_MAX=30;STR_PATHOLOGIC_MIN=50;STR_STATUS=normal;SVTYPE=STR;VARID=CNBP;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:9.0/9.0:39:6-8/6-8:7/7:SPANNING/SPANNING:AR,AD::.:7555:1:U1:gt&gq&only_IP&vim&exit_u1
311
- chr4 39348425 . A <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_002913.5|protein_coding||2/24|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=CANVAS;DisplayRU=ANNNN;END=39348485;HGNCId=9969;REF=12;REPID=RFC1;RL=61;RU=AAAAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=15;STR_PATHOLOGIC_MIN=300;STR_STATUS=normal,normal;SVTYPE=STR;VARID=RFC1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:29/19:51:12-13/9-9:13/9:SPANNING/SPANNING:AR,AD::.:5981:1:U1:gt&gq&only_IP&vim&exit_u1
312
- chr4 41745972 . A <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|3/3||||835-894/2785|720-779/945|240-260/314||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=CCHS;DisplayRU=NGC;END=41746032;HGNCId=9143;REF=20;REPID=PHOX2B;RL=61;RU=GCC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=20;STR_PATHOLOGIC_MIN=25;STR_STATUS=normal;SVTYPE=STR;VARID=PHOX2B;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:20.0/20.0:43:17-20/17-20:19/19:SPANNING/SPANNING:AR,AD::.:8929:1:U1:gt&gq&only_IP&vim&exit_u1
313
- chr5 146878728 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|PPP2R2B|5521|Transcript|NM_181675.4|protein_coding|1/10||||1-29/10828||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA12;DisplayRU=CTG;END=146878757;HGNCId=9305;REF=10;REPID=PPP2R2B;RL=30;RU=GCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=43;STR_STATUS=normal,normal;SVTYPE=STR;VARID=PPP2R2B;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:18/17:35:14-16/10-11:15/11:SPANNING/SPANNING:AR,AD::.:5521:1:U1:gt&gq&only_IP&vim&exit_u1
314
- chr6 45422752 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|RUNX2|860|Transcript|NM_001024630.4|protein_coding|3/9||||416-464/5540|219-267/1566|73-89/521||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=CCD;DisplayRU=GCN;END=45422801;HGNCId=10472;REF=16;REPID=RUNX2;RL=50;RU=GCA;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=17;STR_PATHOLOGIC_MIN=27;STR_STATUS=normal;SVTYPE=STR;VARID=RUNX2;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:18.0/18.0:39:14-15/14-15:15/15:SPANNING/SPANNING:AR,AD::.:860:1:U1:gt&gq&only_IP&vim&exit_u1
315
- chr7 27199679 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|HOXA13|3209|Transcript|NM_000522.5|protein_coding|1/2||||360-412/5015|346-398/1167|116-133/388||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=27199732;REF=18;REPID=HOXA13_III;RL=54;RU=GCG;RUMATCH;SVTYPE=STR;VARID=HOXA13_III;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:48/2:51:16-17/13-13:17/13:SPANNING/SPANNING:AR,AD,AR_C:chr7_27199925_G_/:.:3209:1:U1:gt&gq&only_IP&vim&exit_u1
316
- chr7 27199925 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|HOXA13|3209|Transcript|NM_000522.5|protein_coding|1/2||||126-166/5015|112-152/1167|38-51/388||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=27199966;REF=14;REPID=HOXA13_I;RL=42;RU=GCC;RUMATCH;SVTYPE=STR;VARID=HOXA13_I;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:43/7:52:13-15/7-12:14/11:SPANNING/SPANNING:AR,AD,AR_C:chr7_27199679_C_/:.:3209:1:U1:gt&gq&only_IP&vim&exit_u1
317
- chr8 104588961 . A <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|LRP12|29967|Transcript|NM_013437.5|protein_coding|1/7||||260-297/4378||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=OPDM1;DisplayRU=CCG;END=104588999;HGNCId=31708;REF=13;REPID=LRP12;RL=39;RU=CGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=45;STR_PATHOLOGIC_MIN=90;STR_STATUS=normal,normal;SVTYPE=STR;VARID=LRP12;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:13/19:35:15-16/12-12:16/12:SPANNING/SPANNING:AR,AD::.:29967:1:U1:gt&gq&only_IP&vim&exit_u1
318
- chr9 69037287 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|FXN|2395|Transcript|NM_000144.5|protein_coding||1/4|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=FRDA;DisplayRU=GAA;END=69037304;HGNCId=3951;REF=6;REPID=FXN;RL=18;RU=AAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=34;STR_PATHOLOGIC_MIN=66;STR_STATUS=normal,normal;SVTYPE=STR;VARID=FXN;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:2/23:31:17-17/9-10:17/10:SPANNING/SPANNING:AR,AD::.:2395:1:U1:gt&gq&only_IP&vim&exit_u1
319
- chrX 25013650 . G <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ARX|170302|Transcript|NM_139058.3|protein_coding|2/5||||526-572/2893|298-344/1689|100-115/562||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=25013697;REF=16;REPID=ARX_I;RL=48;RU=GCC;RUMATCH;SVTYPE=STR;VARID=ARX_I;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:19.0/19.0:39:14-15/14-15:15/15:SPANNING/SPANNING:XLD,XLR::.:170302:1:U1:gt&gq&only_IP&vim&exit_u1
320
- chrX 137566828 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ZIC3|7547|Transcript|NM_003413.4|protein_coding|1/3||||703-730/4001|138-165/1404|46-55/467||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=VACTERLX;DisplayRU=GCN;END=137566856;HGNCId=12874;REF=9;REPID=ZIC3;RL=29;RU=CGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=10;STR_PATHOLOGIC_MIN=11;STR_STATUS=normal;SVTYPE=STR;VARID=ZIC3;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:21.5/21.5:45:10-11/10-11:10/10:SPANNING/SPANNING:XLD,XLR::.:7547:1:U1:gt&gq&only_IP&vim&exit_u1
321
- chrX 147912051 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|FMR1|2332|Transcript|NM_002024.6|protein_coding|1/17||||134-192/4441||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=FX;DisplayRU=CGG;END=147912110;HGNCId=3775;REF=20;REPID=FMR1;RL=60;RU=GGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=44;STR_PATHOLOGIC_MIN=200;STR_STATUS=normal;SVTYPE=STR;VARID=FMR1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:20.0/20.0:44:29-31/29-31:30/30:SPANNING/SPANNING:XLD,XLR::.:2332:1:U1:gt&gq&only_IP&vim&exit_u1
291
+ chr1 149390803 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|NOTCH2NLC|100996717|Transcript|NM_001364012.2|protein_coding|1/5||||184-221/8737||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|NOTCH2NLC|100996717|Transcript|NM_001364013.2|protein_coding|1/5||||184-221/8729|17-54/882|6-18/293||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013370||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524215322||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;END=149390841;RU_CALL=GGC;RU_CAT=GGC;RU_CI=13.6-17.4;RU_NR=18.3;RU_SEEN=GGC(20),CGCGCTGCTGTG(11),AAC(1),GCTCAGCTGTCGGCGCGCTGCTG(1);RankScore=1:10;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:33:33:33:AR,AD:100996717:U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
292
+ chr2 190880873 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GLS|2744|Transcript|NM_001256310.2|protein_coding|1/15||||54-100/4488||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GLS|2744|Transcript|NM_014905.5|protein_coding|1/18||||54-100/4840||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000127926||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522155961||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00008164746||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00207535362||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525860781||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00105969646||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=GDPAG;DisplayRU=GCA;END=190880920;HGNCId=4331;InheritanceMode=AR;REPID=GLS;RU_CALL=GCA;RU_CAT=GCA;RU_CI=12.6-13.4;RU_MATCH;RU_NR=13.3;RU_SEEN=GCA(30),AGCCTCAGTGCGG(21);RankScore=1:10;STR_NORMAL_MAX=20;STR_PATHOLOGIC_MIN=90;STR_STATUS=normal;SVTYPE=STR;Source=PubMed;SourceDisplay=van_Kuilenburg_et_al_(2019)_NEJM_380_1433-1441;SourceId=30970188;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:51:51:51:AR,AD:2744:U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
293
+ chr3 63912685 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_000333.4|protein_coding|3/13||||664-692/7250|88-116/2679|30-39/892||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_001177387.1|protein_coding|2/13||||198-226/6851|88-116/2838|30-39/945||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_001377405.1|protein_coding|3/13||||490-518/7076|88-116/2679|30-39/892||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_001377406.1|protein_coding|2/12||||169-197/6755|88-116/2679|30-39/892||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|SCAANT1|100861563|Transcript|NR_148359.1|antisense_RNA|||||||||||1|914|-1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000153622||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00197411295||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00211181983||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=SCA7;DisplayRU=CAG;END=63912714;HGNCId=10560;InheritanceMode=AD;REPID=ATXN7;RU_CALL=GCA;RU_CAT=GCA;RU_CI=11.1-12.1;RU_MATCH;RU_NR=11.7;RU_SEEN=GCCGCGCCGAGCAGCGGCCGCG(2),GGC(1),GCCGCG(1),GCAGCAGCCGCCGCCACCGCAGCCACGGC(1),GCAGCCGCC(1),GCA(39),CAGCCGCCA(1),GCCGCGGCCGCCGGCAGCG(1),GCC(2),GCCGCGCCGCCCCGCGGCGGCGGCGGCAGCAGCAGCG(1),GCGGCCGCGGCCGCCCGGCAGCA(3),CCGCCACCG(1);RankScore=1:10;STR_NORMAL_MAX=19;STR_PATHOLOGIC_MIN=36;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:54:54:54:AR,AD,AR_C:chr3_63912715_G_:100861563,6314:U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
294
+ chr3 63912715 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_000333.4|protein_coding|3/13||||694-704/7250|118-128/2679|40-43/892||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_001177387.1|protein_coding|2/13||||228-238/6851|118-128/2838|40-43/945||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_001377405.1|protein_coding|3/13||||520-530/7076|118-128/2679|40-43/892||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_001377406.1|protein_coding|2/12||||199-209/6755|118-128/2679|40-43/892||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|upstream_gene_variant|MODIFIER|SCAANT1|100861563|Transcript|NR_148359.1|antisense_RNA|||||||||||1|944|-1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000153622||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00000009740||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;END=63912726;REPID=ATXN7_GCC;RU_CALL=GCA;RU_CAT=GCC;RU_CI=5.6-6.5;RU_NR=6.0;RU_SEEN=GCAGCAGCCGCCGCCACCGCAGCCACGGC(1),GCA(42),CCGCGCCGCCCCGCGGCGGCGGCGGCAGCAGCAGCGG(1),GCC(6),GCGGCCGCGGCCGCCCGGCAGCA(3),CGCCGGCAGCGGCCGCGGC(1);SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S ./1:54:54:54:AR,AD,AR_C:chr3_63912685_G_:100861563,6314:U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
295
+ chr3 129172577 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127192.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127193.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127194.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127195.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127196.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_003418.5|protein_coding||1/4|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb;Disease=DM2;DisplayRU=CCTG;END=129172656;HGNCId=13164;InheritanceMode=AD;REPID=CNBP;RU_CALL=CAGA;RU_CAT=CAGG;RU_CI=15.3-16.0;RU_NR=15.8;RU_SEEN=CAGG(2),CAGA(55);RankScore=1:10;STR_NORMAL_MAX=30;STR_PATHOLOGIC_MIN=75;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2020-03-19;SourceId=NBK1466;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/.:57:57:57:AR,AD,AR_C:chr3_129172657_C_,chr3_129172697_C_:7555:U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2
296
+ chr3 129172657 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127192.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127193.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127194.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127195.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127196.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_003418.5|protein_coding||1/4|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus;END=129172696;REPID=CNBP_CAGA;RU_CALL=CAGA;RU_CAT=CAGA;RU_CI=5.7-6.4;RU_MATCH;RU_NR=6.2;RU_SEEN=CAGG(3),CAGA(54);SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:57:57:57:AR,AD,AR_C:chr3_129172577_C_,chr3_129172697_C_:7555:U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2
297
+ chr3 129172697 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127192.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127193.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127194.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127195.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_001127196.2|protein_coding||1/4|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_003418.5|protein_coding||1/4|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus;END=129172732;REPID=CNBP_CA;RU_CALL=CA;RU_CAT=CA;RU_CI=12.1-13.8;RU_MATCH;RU_NR=13.5;RU_SEEN=CA(57);SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:57:57:57:AR,AD,AR_C:chr3_129172577_C_,chr3_129172657_C_:7555:U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2
298
+ chr4 39348425 . A <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_001204747.2|protein_coding||2/24|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lp,tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_001363495.2|protein_coding||2/23|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lp,tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_001363496.2|protein_coding||2/23|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lp,tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_002913.5|protein_coding||2/24|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lp,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000721896||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_001204747.2|protein_coding||2/24|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lp,tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_001363495.2|protein_coding||2/23|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lp,tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_001363496.2|protein_coding||2/23|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lp,tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_002913.5|protein_coding||2/24|||||||||2||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lp,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000721896||||||||||||2|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=CANVAS;DisplayRU=AARRG;END=39348479;HGNCId=9969;InheritanceMode=AR;REPID=RFC1;RU_CALL=AAAAG;RU_CAT=AARRG;RU_CI=112.6-114.6,11.7-12.1;RU_MATCH;RU_NR=114.4,12.0;RU_SEEN=AAAAG(52);RankScore=1:30;STR_NORMAL_MAX=11;STR_PATHOLOGIC_MIN=12;STR_STATUS=full_mutation,full_mutation;SVTYPE=STR;Source=PubMed;SourceDisplay=Cortese_et_al_2019_Nat_Gen;SourceId=30926972;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:29,23:52:29,23:AR,AD:0.557692:5981:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
299
+ chr4 41745973 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|3/3||||835-893/2785|720-778/945|240-260/314||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb;Disease=CCHS;DisplayRU=GCN;END=41746032;HGNCId=9143;InheritanceMode=AD;REPID=PHOX2B;RU_CALL=GCTGCCGCC;RU_CAT=GCN;RU_CI=6.0-6.4;RU_NR=6.3;RU_SEEN=GCCGCCGCTGCCGCGGCCGCC(2),GCTGCCGCC(54),GCCGCA(1),CCGCCGCCC(1),GCC_GCCGCCGCTGCCGCGCCGCC(4);RankScore=1:10;STR_NORMAL_MAX=20;STR_PATHOLOGIC_MIN=25;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2014-01-30;SourceId=NBK1427;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:62:62:62:AR,AD:8929:U2:gt&gq&only_IP&vig&vim&exit_u2
300
+ chr5 146878728 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|PPP2R2B|5521|Transcript|NM_001271899.1|protein_coding||2/9|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|PPP2R2B|5521|Transcript|NM_001271900.2|protein_coding||2/10|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|PPP2R2B|5521|Transcript|NM_001271948.2|protein_coding|1/10||||1-29/11308||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|PPP2R2B|5521|Transcript|NM_181674.3|protein_coding||1/9|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|PPP2R2B|5521|Transcript|NM_181675.4|protein_coding|1/10||||1-29/10828||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|PPP2R2B|5521|Transcript|NM_181676.3|protein_coding||1/8|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|PPP2R2B|5521|Transcript|NM_181677.2|protein_coding||3/10|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|PPP2R2B|5521|Transcript|NM_181678.2|protein_coding||2/10|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|PPP2R2B|5521|Transcript|NR_073526.2|misc_RNA|1/9||||1-29/11223||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|PPP2R2B|5521|Transcript|NR_073527.2|misc_RNA|1/10||||1-29/10718||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001261893||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00195551292||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=SCA12;DisplayRU=CAG;END=146878757;HGNCId=9305;InheritanceMode=AD;REPID=PPP2R2B;RU_CALL=GCT;RU_CAT=GCT;RU_CI=9.9-10.5;RU_MATCH;RU_NR=10.3;RU_SEEN=GCGCGCACCCCC(1),GCTGCTGCAGGAGGCGAGGCG(1),AGCTGGCGGGG(1),GGAGCTGGCAG(1),GCT_GGGAGCTGGGCA(1),GCT(30),GCTGGAGGCG(1),CGCGCGCACTCACA(1),AGCTGGCAGGG(2),CGCACT(1);RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=51;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:40:40:40:AR,AD:5521:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
301
+ chr6 16327634 . T <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN1|6310|Transcript|NM_000332.4|protein_coding|8/9||||1529-1617/10606|588-676/2448|196-226/815||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN1|6310|Transcript|NM_001128164.2|protein_coding|7/8||||1480-1568/10557|588-676/2448|196-226/815||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|ATXN1|6310|Transcript|NM_001357857.2|protein_coding|8/9||||1529-1617/10606||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|downstream_gene_variant|MODIFIER|LOC127903862|127903862|Transcript|NM_001414722.1|protein_coding|||||||||||1|619|-1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb;Disease=SCA1;DisplayRU=CAG;END=16327723;HGNCId=10548;InheritanceMode=AD;REPID=ATXN1;RU_CALL=TGC;RU_CAT=TGC;RU_CI=30.3-30.8;RU_MATCH;RU_NR=30.8;RU_SEEN=TGC(40);RankScore=1:10;STR_NORMAL_MAX=35;STR_PATHOLOGIC_MIN=45;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2017-06-22;SourceId=NBK1184;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:40:40:40:AR,AD:6310:U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
302
+ chr6 170561907 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|TBP|6908|Transcript|NM_001172085.2|protein_coding|2/7||||213-322/1655|112-221/960|38-74/319||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|TBP|6908|Transcript|NM_003194.5|protein_coding|3/8||||415-524/1857|172-281/1020|58-94/339||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001120219||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=SCA17;DisplayRU=CAN;END=170562017;HGNCId=11588;InheritanceMode=AD;REPID=TBP;RU_CALL=GCA;RU_CAT=GCA;RU_CI=35.9-36.5;RU_MATCH;RU_NR=36.0;RU_SEEN=GCA(40);RankScore=1:10;STR_NORMAL_MAX=40;STR_PATHOLOGIC_MIN=49;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-09-12;SourceId=NBK1438;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:40:40:40:AR,AD:6908:U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
303
+ chr9 69037262 . A <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|FXN|2395|Transcript|NM_000144.5|protein_coding||1/4|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant|HIGH|FXN|2395|Transcript|NM_181425.3|protein_coding||1/4|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus;END=69037286;REPID=FXN_A;RU_CALL=AAAAAAGA;RU_CAT=A;RU_CI=3.9-4.5;RU_NR=4.1;RU_SEEN=TACAAAAAAA(2),AAAATAAAGAAAGAAGAAG(1),AAAAGAAGA(2),AAAAAAAAGAAAAGAAG(1),AAAAAAGA(27),AAG(1),AAAAAAAAGAAAAAGAAAG_AAAAAG(1);SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:35:35:35:AR,AD,AR_C:chr9_69037287_G_:2395:U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2
304
+ chr9 69037287 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|FXN|2395|Transcript|NM_000144.5|protein_coding||1/4|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|FXN|2395|Transcript|NM_181425.3|protein_coding||1/4|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb;Disease=FRDA;DisplayRU=GAA;END=69037304;HGNCId=3951;InheritanceMode=AR;REPID=FXN;RU_CALL=AAAAAAGA;RU_CAT=GAA;RU_CI=3.6-4.9;RU_NR=3.5;RU_SEEN=TACAAAAAAA(2),AAAAAAGA(27),GAA(5),AAAAAAAAGAAAAAGAAAG_AAAAAG(1);RankScore=1:10;STR_NORMAL_MAX=35;STR_PATHOLOGIC_MIN=51;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:35:35:35:AR,AD,AR_C:chr9_69037262_A_:2395:U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2
305
+ chr12 6936717 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATN1|1822|Transcript|NM_001007026.2|protein_coding|5/10||||1692-1747/4355|1451-1506/3573|484-502/1190||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATN1|1822|Transcript|NM_001940.4|protein_coding|5/10||||2039-2094/4702|1451-1506/3573|484-502/1190||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000048373||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=DRPLA;DisplayRU=CAG;END=6936773;HGNCId=3033;InheritanceMode=AD;REPID=ATN1;RU_CALL=CAG;RU_CAT=CAG;RU_CI=17.5-18.3;RU_MATCH;RU_NR=17.7;RU_SEEN=CAG(49);RankScore=1:10;STR_NORMAL_MAX=35;STR_PATHOLOGIC_MIN=48;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:49:49:49:AR,AD:1822:U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
306
+ chr12 111598950 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN2|6311|Transcript|NM_001310121.1|protein_coding||1/25|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN2|6311|Transcript|NM_001310123.1|protein_coding||1/21|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN2|6311|Transcript|NM_001372574.1|protein_coding|1/25||||298-365/4347|17-84/3468|6-28/1155||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN2|6311|Transcript|NM_002973.4|protein_coding|1/25||||298-365/4341|17-84/3462|6-28/1153||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN2|6311|Transcript|NR_132311.2|misc_RNA|1/24||||298-365/4280||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|ATXN2-AS|102723619|Transcript|NR_146497.1|lncRNA|||||||||||1|480|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000057455||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN2|6311|Transcript|NM_001310121.1|protein_coding||1/25|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN2|6311|Transcript|NM_001310123.1|protein_coding||1/21|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN2|6311|Transcript|NM_001372574.1|protein_coding|1/25||||298-365/4347|17-84/3468|6-28/1155||||2||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN2|6311|Transcript|NM_002973.4|protein_coding|1/25||||298-365/4341|17-84/3462|6-28/1153||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN2|6311|Transcript|NR_132311.2|misc_RNA|1/24||||298-365/4280||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|ATXN2-AS|102723619|Transcript|NR_146497.1|lncRNA|||||||||||2|480|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000057455||||||||||||2|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=SCA2;DisplayRU=CAG;END=111599018;HGNCId=10555;InheritanceMode=AD;REPID=ATXN2;RU_CALL=GCT;RU_CAT=GCT;RU_CI=21.7-22.3,29.9-30.5;RU_MATCH;RU_NR=22.0,30.3;RU_SEEN=GCT(63);RankScore=1:10;STR_NORMAL_MAX=31;STR_PATHOLOGIC_MIN=37;STR_STATUS=normal,normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-02-14;SourceId=NBK1275;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:31,32:63:31,32:AR,AD:0.492063:6311:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
307
+ chr13 70139354 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN8OS|6315|Transcript|NR_002717.2|antisense_RNA|5/5||||1074-1102/1472||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus;END=70139383;REPID=ATXN8OS_CTA;RU_CALL=CTG;RU_CAT=CTA;RU_CI=9.5-10.4;RU_NR=9.8;RU_SEEN=CTA(1),CTG(38),TCTATTTA(1);SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:40:40:40:AR,AD,AR_C:chr13_70139384_C_:6315:U2:gt&gq&only_IP&vig&vim&exit_u2
308
+ chr13 70139384 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN8OS|6315|Transcript|NR_002717.2|antisense_RNA|5/5||||1104-1147/1472||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb;Disease=SCA8;DisplayRU=CTG;END=70139428;HGNCId=10561;InheritanceMode=AD;REPID=ATXN8OS;RU_CALL=CTG;RU_CAT=CTG;RU_CI=14.3-15.3;RU_MATCH;RU_NR=14.8;RU_SEEN=TAC(1),CTG(38),TCTATTTA(1);RankScore=1:10;STR_NORMAL_MAX=50;STR_PATHOLOGIC_MIN=80;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:40:40:40:AR,AD,AR_C:chr13_70139354_C_:6315:U2:gt&gq&only_IP&vig&vim&exit_u2
309
+ chr14 23321473 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|BCL2L2-PABPN1|100529063|Transcript|NM_001199864.3|protein_coding||3/8|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|PABPN1|8106|Transcript|NM_001360551.3|protein_coding|1/6||||18-34/2768|5-21/891|2-7/296||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|PABPN1|8106|Transcript|NM_001360552.2|protein_coding|||||||||||1|516|1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|BCL2L2-PABPN1|100529063|Transcript|NM_001387340.1|protein_coding||4/9|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|BCL2L2-PABPN1|100529063|Transcript|NM_001387341.1|protein_coding||4/9|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|BCL2L2-PABPN1|100529063|Transcript|NM_001387342.1|protein_coding||4/9|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|BCL2L2-PABPN1|100529063|Transcript|NM_001387343.1|protein_coding||4/8|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|BCL2L2-PABPN1|100529063|Transcript|NM_001387344.1|protein_coding||4/8|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|BCL2L2-PABPN1|100529063|Transcript|NM_001387345.1|protein_coding||3/7|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|BCL2L2-PABPN1|100529063|Transcript|NM_001387346.1|protein_coding||3/7|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|PABPN1|8106|Transcript|NM_004643.4|protein_coding|1/7||||18-34/1811|5-21/921|2-7/306||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000066726||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=OPMD;DisplayRU=GCN;END=23321490;HGNCId=8565;InheritanceMode=AD;REPID=PABPN1;RU_CALL=GCG;RU_CAT=GCG;RU_CI=5.9-6.5;RU_MATCH;RU_NR=6.3;RU_SEEN=GGGCGGCGGGCCCCAGTCAGAGCGGGCGATGCGGGCGGGGC(1),GCGGGGGCT(1),GCG(42);RankScore=1:10;STR_NORMAL_MAX=10;STR_PATHOLOGIC_MIN=11;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2020-10-22;SourceId=NBK1126;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:44:44:44:AR,AD:8106:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
310
+ chr14 92071010 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001127696.2|protein_coding|9/10||||869-900/6839|839-870/1041|280-290/346||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001127697.3|protein_coding|8/9||||761-792/6731|731-762/933|244-254/310||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001164774.2|protein_coding|3/4||||231-262/6201|201-232/267|67-78/88||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001164776.2|protein_coding|4/5||||276-307/6246|246-277/312|82-93/103||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001164777.2|protein_coding|3/4||||111-142/6081|81-112/147|27-38/48||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001164778.2|protein_coding|6/7||||429-460/6399|399-430/465|133-144/154||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001164779.2|protein_coding|6/7||||551-582/6521|521-552/723|174-184/240||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001164780.2|protein_coding|7/8||||618-649/6588|347-378/549|116-126/182||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001164781.2|protein_coding|8/9||||704-735/6674|674-705/876|225-235/291||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_001164782.2|protein_coding|2/3||||66-97/6036|36-67/102|12-23/33||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_004993.6|protein_coding|10/11||||914-945/6884|884-915/1086|295-305/361||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_030660.5|protein_coding|9/10||||749-780/6719|719-750/921|240-250/306||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028453.2|misc_RNA|9/10||||828-859/6798||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028454.2|misc_RNA|8/9||||663-694/6633||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028455.2|misc_RNA|10/11||||882-913/6852||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028456.2|misc_RNA|9/10||||717-748/6687||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028457.2|misc_RNA|11/12||||973-1004/6943||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028458.2|misc_RNA|9/10||||817-848/6787||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028459.2|misc_RNA|11/12||||968-999/6938||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028460.2|misc_RNA|5/6||||343-374/6313||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028461.2|misc_RNA|9/10||||826-857/6796||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028462.2|misc_RNA|9/10||||805-836/6775||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028463.2|misc_RNA|6/7||||517-548/6487||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028464.2|misc_RNA|9/10||||815-846/6785||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028465.2|misc_RNA|9/10||||837-868/6807||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028466.2|misc_RNA|5/6||||463-494/6433||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028467.2|misc_RNA|9/10||||829-860/6799||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028468.2|misc_RNA|8/9||||661-692/6631||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028469.2|misc_RNA|8/9||||675-706/6645||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_028470.2|misc_RNA|3/4||||133-164/6103||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN3|4287|Transcript|NR_031765.2|misc_RNA|4/5||||330-361/6300||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb;Disease=MJD;DisplayRU=CAG;END=92071042;HGNCId=7106;InheritanceMode=AD;REPID=ATXN3;RU_CALL=CTG;RU_CAT=GCT;RU_CI=20.9-22.2;RU_MATCH;RU_NR=21.7;RU_SEEN=CTG(50);RankScore=1:10;STR_NORMAL_MAX=44;STR_PATHOLOGIC_MIN=60;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:50:50:50:AR,AD:4287:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2
311
+ chr15 22786678 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|NIPA1|123606|Transcript|NM_001142275.1|protein_coding||1/4|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|NIPA1|123606|Transcript|NM_144599.5|protein_coding|1/5||||36-58/6553|23-45/990|8-15/329||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000073999||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=ALS_-_susceptibility_to;DisplayRU=GCG;END=22786701;HGNCId=17043;InheritanceMode=AD;REPID=NIPA1;RU_CALL=GCG;RU_CAT=GCG;RU_CI=10.3-11.8;RU_MATCH;RU_NR=12.7;RU_SEEN=GCAGCGGCG_GGGC(1),GCG(37),GGCGCGGCGCGCA(1);RankScore=1:20;STR_NORMAL_MAX=8;STR_PATHOLOGIC_MIN=10000;STR_STATUS=pre_mutation;SVTYPE=STR;Source=PubMed;SourceDisplay=Tazelaar_et_al_(2019)_Neurobiol_Aging_74_234.e9-234.e15;SourceId=30342764;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:39:39:39:AR,AD:123606:U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
312
+ chr16 87604288 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|JPH3|57338|Transcript|NM_001271604.4|protein_coding|2/2||||1071-1111/1410|432-472/561|144-158/186||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|JPH3|57338|Transcript|NM_001271605.3|protein_coding|2/2||||1222-1262/1561||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|JPH3|57338|Transcript|NM_020655.4|protein_coding||1/4|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant&non_coding_transcript_variant|HIGH|JPH3|57338|Transcript|NR_073379.3|misc_RNA||1/5|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb;Disease=HDL2;DisplayRU=CTG;END=87604329;HGNCId=14203;InheritanceMode=AD;REPID=JPH3;RU_CALL=CTG;RU_CAT=CTG;RU_CI=15.7-16.4;RU_MATCH;RU_NR=16.0;RU_SEEN=CTG(37);RankScore=1:10;STR_NORMAL_MAX=28;STR_PATHOLOGIC_MIN=40;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-06-27;SourceId=NBK1529;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:37:37:37:AR,AD:57338:U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2
313
+ chr18 55586156 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001083962.2|protein_coding||2/19|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001243226.3|protein_coding||3/20|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001243227.2|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001243228.2|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001243230.2|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001306207.1|protein_coding|||||||||||1|38|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001330604.3|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001348217.1|protein_coding|||||||||||1|38|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001348218.2|protein_coding|||||||||||1|35|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001348219.2|protein_coding|||||||||||1|35|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001348220.1|protein_coding|||||||||||1|38|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369567.1|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369568.1|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369569.1|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369570.1|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369571.1|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369572.1|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369573.1|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369574.1|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369575.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369576.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369577.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369578.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369579.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001369580.1|protein_coding|||||||||||1|35|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001369581.1|protein_coding|||||||||||1|35|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369582.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369583.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369584.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369585.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369586.1|protein_coding||1/18|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_003199.3|protein_coding||2/19|||||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000103605||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001083962.2|protein_coding||2/19|||||||||2||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001243226.3|protein_coding||3/20|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001243227.2|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001243228.2|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001243230.2|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001306207.1|protein_coding|||||||||||2|38|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001330604.3|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001348217.1|protein_coding|||||||||||2|38|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001348218.2|protein_coding|||||||||||2|35|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001348219.2|protein_coding|||||||||||2|35|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001348220.1|protein_coding|||||||||||2|38|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369567.1|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369568.1|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369569.1|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369570.1|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369571.1|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369572.1|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369573.1|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369574.1|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369575.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369576.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369577.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369578.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369579.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001369580.1|protein_coding|||||||||||2|35|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|TCF4|6925|Transcript|NM_001369581.1|protein_coding|||||||||||2|35|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369582.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369583.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369584.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369585.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001369586.1|protein_coding||1/18|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_003199.3|protein_coding||2/19|||||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000103605||||||||||||2|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=FECD3;DisplayRU=CTG;END=55586227;HGNCId=11634;InheritanceMode=AD;REPID=TCF4;RU_CALL=CAG;RU_CAT=CAG;RU_CI=12.7-13.9,31.6-32.3;RU_MATCH;RU_NR=13.3,32.3;RU_SEEN=GGA(1),GAGGAGAGGAGGAGCAG(1),CAG(52);RankScore=1:10;STR_NORMAL_MAX=39;STR_PATHOLOGIC_MIN=100;STR_STATUS=normal,normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:25,29:54:25,29:AR,AD:0.462963:6925:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
314
+ chr19 13207859 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|CACNA1A|773|Transcript|NM_000068.4|protein_coding|48/48||||7205-7242/8660||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|CACNA1A|773|Transcript|NM_001127221.2|protein_coding|47/47||||7190-7227/8645||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|CACNA1A|773|Transcript|NM_001127222.2|protein_coding|47/47||||7192-7229/8647|6937-6974/7521|2313-2325/2506||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|CACNA1A|773|Transcript|NM_001174080.2|protein_coding|48/48||||7196-7233/8651||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|CACNA1A|773|Transcript|NM_023035.3|protein_coding|48/48||||7210-7247/8665|6955-6992/7539|2319-2331/2512||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb;Disease=SCA6;DisplayRU=CAG;END=13207897;HGNCId=1388;InheritanceMode=AD;REPID=CACNA1A;RU_CALL=CTG;RU_CAT=CTG;RU_CI=10.5-11.2;RU_MATCH;RU_NR=11.0;RU_SEEN=CTG(62),TGGCCCGCC(1);RankScore=1:10;STR_NORMAL_MAX=18;STR_PATHOLOGIC_MIN=20;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:63:63:63:AR,AD:773:U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2
315
+ chr19 14496042 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_005716.4|protein_coding|1/9||||54-85/1921||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_202468.3|protein_coding|1/8||||54-85/1865||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_202469.3|protein_coding|1/7||||54-85/1547||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_202470.3|protein_coding|1/7||||54-85/1777||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_202494.3|protein_coding|1/6||||54-85/1459||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000107548||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524479476||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523228879||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00202330410||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522098195||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00180296361||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_005716.4|protein_coding|1/9||||54-85/1921||||||2||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_202468.3|protein_coding|1/8||||54-85/1865||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_202469.3|protein_coding|1/7||||54-85/1547||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_202470.3|protein_coding|1/7||||54-85/1777||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_202494.3|protein_coding|1/6||||54-85/1459||||||2||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000107548||||||||||||2|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524479476||||||||||||2|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523228879||||||||||||2|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00202330410||||||||||||2|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522098195||||||||||||2|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00180296361||||||||||||2|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=OPDM2;DisplayRU=GGC;END=14496074;HGNCId=1226;InheritanceMode=AD;REPID=GIPC1;RU_CALL=CCG;RU_CAT=CCG;RU_CI=11.3-12.6,15.7-15.7;RU_MATCH;RU_NR=11.0,15.7;RU_SEEN=CCGCCGCAGCCTCCGCCTCC(1),CCG(57);RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=73;STR_STATUS=normal,normal;SVTYPE=STR;Source=PubMed;SourceDisplay=Deng_et_al_2020_AJHG_106(6)_793-804;SourceId=32413282;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:38,20:58:38,20:AR,AD:0.655172:10755:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
316
+ chr19 45770205 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_001081560.3|protein_coding|15/15||||2237-2295/2784||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_001081562.3|protein_coding|15/15||||2233-2291/2780||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_001081563.2|protein_coding|14/14||||2688-2746/3243||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_001288764.2|protein_coding|16/16||||2311-2369/2858||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_001288765.2|protein_coding|13/13||||1955-2013/2502||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_001288766.2|protein_coding|13/13||||2100-2158/2647||||||1||-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_004409.5|protein_coding|15/15||||2252-2310/2799||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|SIX5|147912|Transcript|NM_175875.5|protein_coding|||||||||||1|954|-1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant&non_coding_transcript_variant|HIGH|DM1-AS|109729182|Transcript|NR_147193.1|lncRNA||1/1|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001221403||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000591473||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00207169291||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00087660738||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522701496||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00207195006||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00521947908||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=DM1;DisplayRU=CTG;END=45770264;HGNCId=2933;InheritanceMode=AD;REPID=DMPK;RU_CALL=CAG;RU_CAT=CAG;RU_CI=10.7-11.3;RU_MATCH;RU_NR=11.3;RU_SEEN=CAG(40);RankScore=1:10;STR_NORMAL_MAX=34;STR_PATHOLOGIC_MIN=50;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-10-03;SourceId=NBK1165;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:40:40:40:AR,AD:147912,1760:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
317
+ chr20 2652734 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|NOP56|10528|Transcript|NM_006392.4|protein_coding||1/11|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|SNORD57|26792|Transcript|NR_002738.1|snoRNA|||||||||||1|4182|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|SNORD56|26793|Transcript|NR_002739.1|snoRNA|||||||||||1|3867|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|SNORA51|677831|Transcript|NR_002981.1|snoRNA|||||||||||1|2310|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|SNORD110|692213|Transcript|NR_003078.1|snoRNA|||||||||||1|1455|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|SNORD86|692201|Transcript|NR_004399.1|snoRNA|||||||||||1|3340|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant&non_coding_transcript_variant|HIGH|NOP56|10528|Transcript|NR_027700.3|misc_RNA||1/11|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|MIR1292|100302138|Transcript|NR_031699.1|miRNA|||||||||||1|20|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant&non_coding_transcript_variant|HIGH|NOP56|10528|Transcript|NR_145428.2|misc_RNA||1/12|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000133685||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190349373||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=SCA36;DisplayRU=GGCCTG;END=2652757;HGNCId=15911;InheritanceMode=AD;REPID=NOP56;RU_CALL=GGCCTG;RU_CAT=GGCCTG;RU_CI=5.5-6.1;RU_MATCH;RU_NR=5.4;RU_SEEN=GGCCTG(47),GGCCTGCGCCGGGCCTGAGACAGAGCCTG(1);RankScore=1:10;STR_NORMAL_MAX=14;STR_PATHOLOGIC_MIN=650;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2014-08-07;SourceId=NBK231880;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:48:48:48:AR,AD,AR_C:chr20_2652758_C_:100302138,10528,26792,26793,677831,692201,692213:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
318
+ chr20 2652758 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|NOP56|10528|Transcript|NM_006392.4|protein_coding||1/11|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|upstream_gene_variant|MODIFIER|SNORD57|26792|Transcript|NR_002738.1|snoRNA|||||||||||1|4164|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|upstream_gene_variant|MODIFIER|SNORD56|26793|Transcript|NR_002739.1|snoRNA|||||||||||1|3849|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|upstream_gene_variant|MODIFIER|SNORA51|677831|Transcript|NR_002981.1|snoRNA|||||||||||1|2292|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|upstream_gene_variant|MODIFIER|SNORD110|692213|Transcript|NR_003078.1|snoRNA|||||||||||1|1437|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|upstream_gene_variant|MODIFIER|SNORD86|692201|Transcript|NR_004399.1|snoRNA|||||||||||1|3322|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant&non_coding_transcript_variant|HIGH|NOP56|10528|Transcript|NR_027700.3|misc_RNA||1/11|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|upstream_gene_variant|MODIFIER|MIR1292|100302138|Transcript|NR_031699.1|miRNA|||||||||||1|2|1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|feature_elongation&intron_variant&non_coding_transcript_variant|HIGH|NOP56|10528|Transcript|NR_145428.2|misc_RNA||1/12|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_vus,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000133685||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190349373||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;END=2652775;REPID=NOP56_CGCCTG;RU_CALL=CGCCTG;RU_CAT=CGCCTG;RU_CI=4.6-5.5;RU_MATCH;RU_NR=4.4;RU_SEEN=GCCT_GCCTGCCT(1),GGCCTGCGCCGGGCCTGAGACAGAGCCTG(1),CGCCTG(46);SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:48:48:48:AR,AD,AR_C:chr20_2652734_G_:100302138,10528,26792,26793,677831,692201,692213:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
319
+ chr21 43776444 . C <CNV:TR1> . PASS CSQ=tandem_duplication|upstream_gene_variant|MODIFIER|CSTB|1476|Transcript|NM_000100.4|protein_coding|||||||||||1|137|-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000142954||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm,tandem_duplication|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522985565||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=EPM1;DisplayRU=CCCCGCCCCGCG;END=43776479;HGNCId=2482;InheritanceMode=AR;REPID=CSTB;RU_CALL=CGCGGGGCGGGG;RU_CAT=CGCGGGGCGGGG;RU_CI=2.3-2.6;RU_MATCH;RU_NR=2.5;RU_SEEN=GGGCG_GGGCGG_GGGCGGG(1),GCGCAGGGGCGGG_GCGCGGG(1),GCGCGGGGGGCGGGG(1),CGCGGGGCGGGG(36),GCGCGGG_GCGGG(1),GGGACGCGC(1),GCGGGGAC(1),GGGCGGGGAGCC_GGGGCGC(1);RankScore=1:10;STR_NORMAL_MAX=3;STR_PATHOLOGIC_MIN=30;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:43:43:43:AR,AD:1476:U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
320
+ chr22 45795355 . A <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN10|25814|Transcript|NM_001167621.2|protein_coding||8/10|||||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN10|25814|Transcript|NM_013236.4|protein_coding||9/11|||||||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN10|25814|Transcript|NM_001167621.2|protein_coding||8/10|||||||||2||1|||EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN10|25814|Transcript|NM_013236.4|protein_coding||9/11|||||||||2||1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb;Disease=SCA10;DisplayRU=ATTCT;END=45795424;HGNCId=10549;InheritanceMode=AD;REPID=ATXN10;RU_CALL=ATTCT;RU_CAT=ATTCT;RU_CI=15.9-16.1,11.2-11.9;RU_MATCH;RU_NR=16.0,11.8;RU_SEEN=ATTCT(42),ATTCTATTCTATTTTATCTTCATTTC(1);RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=800;STR_STATUS=normal,normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:18,25:43:18,25:AR,AD:0.418605:25814:U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2
321
+ chrX 67545317 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|AR|367|Transcript|NM_000044.6|protein_coding|1/8||||1298-1365/10667|172-239/2763|58-80/920||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|AR|367|Transcript|NM_001011645.3|protein_coding|1/9||||696-763/10252||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|AR|367|Transcript|NM_001348061.1|protein_coding|1/4||||696-763/3812|172-239/1935|58-80/644||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|AR|367|Transcript|NM_001348063.1|protein_coding|1/4||||696-763/2612|172-239/1947|58-80/648||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|AR|367|Transcript|NM_001348064.1|protein_coding|1/3||||696-763/3729|172-239/1719|58-80/572||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000246918||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=SBMA;DisplayRU=CAG;END=67545385;HGNCId=644;InheritanceMode=XR;REPID=AR;RU_CALL=GCA;RU_CAT=GCA;RU_CI=26.2-27.4;RU_MATCH;RU_NR=27.0;RU_SEEN=GCA(18);RankScore=1:10;STR_NORMAL_MAX=34;STR_PATHOLOGIC_MIN=38;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1:18:18:18:XLD,XLR:367:U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
322
+ chrX 147912051 . C <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|FMR1|2332|Transcript|NM_001185075.2|protein_coding|1/16||||134-192/4170||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||1|XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|FMR1|2332|Transcript|NM_001185076.2|protein_coding|1/16||||134-192/4378||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||1|XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|FMR1|2332|Transcript|NM_001185081.2|protein_coding|1/15||||134-192/4107||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||1|XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|FMR1|2332|Transcript|NM_001185082.2|protein_coding|1/16||||134-192/4303||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||1|XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|FMR1|2332|Transcript|NM_002024.6|protein_coding|1/17||||134-192/4441||||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|FMR1-AS1|100126270|Transcript|NR_024499.3|lncRNA|||||||||||1|235|-1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|FMR1-AS1|100126270|Transcript|NR_024501.3|lncRNA|||||||||||1|235|-1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|FMR1-AS1|100126270|Transcript|NR_024502.3|lncRNA|||||||||||1|235|-1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|upstream_gene_variant|MODIFIER|FMR1-AS1|100126270|Transcript|NR_024503.3|lncRNA|||||||||||1|235|-1|||EntrezGene||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|FMR1|2332|Transcript|NR_033699.2|misc_RNA|1/16||||134-192/4245||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||1|XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|FMR1|2332|Transcript|NR_033700.2|misc_RNA|1/15||||134-192/4182||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||1|XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000249258||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=FragileX;DisplayRU=CGG;END=147912110;HGNCId=3775;InheritanceMode=XR;REPID=FMR1;RU_CALL=CGG;RU_CAT=CGG;RU_CI=30.5-31.4;RU_MATCH;RU_NR=31.2;RU_SEEN=CGG(30);RankScore=1:10;STR_NORMAL_MAX=55;STR_PATHOLOGIC_MIN=200;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-21;SourceId=NBK1384;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1:30:30:30:XLD,XLR:2332:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vid&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2
323
+ chrX 148500632 . G <CNV:TR1> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|AFF2|2334|Transcript|NM_001169122.2|protein_coding|1/20||||17-75/13643||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|AFF2|2334|Transcript|NM_001169123.2|protein_coding|1/21||||17-75/13718||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|AFF2|2334|Transcript|NM_001169124.2|protein_coding|1/20||||17-75/13643||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|AFF2|2334|Transcript|NM_001169125.2|protein_coding|1/20||||17-75/13631||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|AFF2|2334|Transcript|NM_002025.4|protein_coding|1/21||||17-75/13748||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||||||||LB|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&str_status&exit_lb,tandem_duplication|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000249272||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|filter&vkgl&clinVar&chrom&gene&exit_rm;Disease=Fraxe;DisplayRU=CCG;END=148500691;HGNCId=3776;InheritanceMode=XR;REPID=AFF2;RU_CALL=GCC;RU_CAT=GCC;RU_CI=18.4-19.1;RU_MATCH;RU_NR=19.3;RU_SEEN=GCC(26);RankScore=1:10;STR_NORMAL_MAX=39;STR_PATHOLOGIC_MIN=200;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1:26:26:26:XLD,XLR:2334:U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vim&exit_u2,gt&gq&only_IP&vig&vid&exit_u2