@molgenis/vip-report-template 8.2.2 → 8.3.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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 +4 -2
  6. package/src/components/field/composed/FieldSpanningReads.tsx +18 -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 +71 -238
  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 +15 -3
  15. package/src/utils/config/configCellsComposed.ts +94 -19
  16. package/src/utils/config/configValidator.precompiled.ts +80 -0
  17. package/tests/utils/config/configCellsComposed.test.ts +70 -35
package/src/mocks/GRCh38/vcf/str.vcf CHANGED
@@ -4,20 +4,22 @@
4
4
  ##ASV_ACMG_class=AnnotSv 'ACMG_class' output.
5
5
  ##ASV_AnnotSV_ranking_criteria=AnnotSv 'AnnotSV_ranking_criteria' output.
6
6
  ##ASV_AnnotSV_ranking_score=AnnotSv 'AnnotSV_ranking_score' output.
7
+ ##ASV_Gene_name=AnnotSv 'Gene_name' output.
8
+ ##ASV_RE_gene=AnnotSv 'RE_gene' output.
7
9
  ##CAPICE_CL=CAPICE classification
8
10
  ##CAPICE_SC=CAPICE score
9
- ##FATHMM_MKL_NC=FATHMM_MKL_NC: Predict the Functional Consequences of Non-Coding Single Nucleotide VariantsRedirect (SNVs)
10
- ##FILTER=<ID=LowDepth,Description="The overall locus depth is below 10x or number of reads spanning one or both breakends is below 5">
11
+ ##FATHMM_MKL_NC=FATHMM_MKL_NC: Predict the Functional Consequences of Non-Coding Single Nucleotide Variants (SNVs)
11
12
  ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
12
- ##FORMAT=<ID=ADFL,Number=1,Type=String,Description="Number of flanking reads consistent with the allele">
13
- ##FORMAT=<ID=ADIR,Number=1,Type=String,Description="Number of in-repeat reads consistent with the allele">
14
- ##FORMAT=<ID=ADSP,Number=1,Type=String,Description="Number of spanning reads consistent with the allele">
15
13
  ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
16
- ##FORMAT=<ID=LC,Number=1,Type=Float,Description="Locus coverage">
17
- ##FORMAT=<ID=REPCI,Number=1,Type=String,Description="Confidence interval for REPCN">
18
- ##FORMAT=<ID=REPCN,Number=1,Type=String,Description="Number of repeat units spanned by the allele">
19
- ##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">
14
+ ##FORMAT=<ID=LC,Number=1,Type=Integer,Description="Locus coverage">
15
+ ##FORMAT=<ID=RU_CALL,Number=1,Type=String,Description="Most frequent actual repeat motif">
16
+ ##FORMAT=<ID=RU_CI,Number=A,Type=String,Description="95% confidence interval per allele. 'NA' if less than 2 reads were present.">
17
+ ##FORMAT=<ID=RU_MATCH,Number=1,Type=Integer,Description="RU call matches catalog (allowing shift/IUPAC), 1=match, 0=mismatch">
18
+ ##FORMAT=<ID=RU_NR,Number=A,Type=String,Description="Number of repeat units per allele.">
19
+ ##FORMAT=<ID=RU_SEEN,Number=.,Type=String,Description="All RUs encountered with read counts">
20
+ ##FORMAT=<ID=RU_SPAN,Number=A,Type=Integer,Description="Number of spanning reads per allele.">
20
21
  ##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">
22
+ ##FORMAT=<ID=VIAB,Number=1,Type=Float,Description="VIP calculated allele balance">
21
23
  ##FORMAT=<ID=VIC,Number=1,Type=String,Description="Possible Compound hetrozygote variants.">
22
24
  ##FORMAT=<ID=VID,Number=1,Type=Integer,Description="De novo variant.">
23
25
  ##FORMAT=<ID=VIG,Number=.,Type=String,Description="Genes with a (potential) inheritance match.">
@@ -25,18 +27,15 @@
25
27
  ##FORMAT=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
26
28
  ##FORMAT=<ID=VIPP_S,Number=.,Type=String,Description="VIP decision tree path.">
27
29
  ##Grantham=Grantham Matrix score - Grantham, R. Amino Acid Difference Formula to Help Explain Protein Evolution, Science 1974 Sep 6;185(4154):862-4.
28
- ##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">
30
+ ##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|hmtvar_DiseaseScore|phyloP|VIPC|VIPP">
29
31
  ##INFO=<ID=Disease,Number=1,Type=String,Description="Associated disorder">
30
32
  ##INFO=<ID=DisplayRU,Number=1,Type=String,Description="Display repeat unit familiar to clinician">
31
- ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
33
+ ##INFO=<ID=END,Number=1,Type=Integer,Description="End position">
32
34
  ##INFO=<ID=HGNCId,Number=1,Type=Integer,Description="HGNC gene id for associated disease gene">
33
35
  ##INFO=<ID=InheritanceMode,Number=1,Type=String,Description="Main mode of inheritance for disorder">
34
36
  ##INFO=<ID=OLD_REC,Number=1,Type=String,Description="Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX">
35
- ##INFO=<ID=REF,Number=1,Type=Integer,Description="Reference copy number">
36
- ##INFO=<ID=REPID,Number=1,Type=String,Description="Repeat identifier as specified in the variant catalog">
37
- ##INFO=<ID=RL,Number=1,Type=Integer,Description="Reference length in bp">
38
- ##INFO=<ID=RU,Number=1,Type=String,Description="Repeat unit in the reference orientation">
39
- ##INFO=<ID=RUMATCH,Number=0,Type=Flag,Description="Flag indicating if the called repeat unit matched the repeat unit in the loci bed file.">
37
+ ##INFO=<ID=REPID,Number=1,Type=String,Description="Locus identifier.">
38
+ ##INFO=<ID=RU_CAT,Number=1,Type=String,Description="Catalog repeat motif">
40
39
  ##INFO=<ID=RankScore,Number=1,Type=String,Description="RankScore for variant in this family as family(str):score(int)">
41
40
  ##INFO=<ID=STR_NORMAL_MAX,Number=1,Type=Integer,Description="Max number of repeats allowed to call as normal">
42
41
  ##INFO=<ID=STR_PATHOLOGIC_MIN,Number=1,Type=Integer,Description="Min number of repeats required to call as pathologic">
@@ -47,11 +46,10 @@
47
46
  ##INFO=<ID=SourceId,Number=1,Type=String,Description="Source id for variant definition">
48
47
  ##INFO=<ID=SweGenMean,Number=1,Type=Float,Description="Average number of repeat unit copies in population">
49
48
  ##INFO=<ID=SweGenStd,Number=1,Type=Float,Description="Standard deviation of number of repeat unit copies in population">
50
- ##INFO=<ID=VARID,Number=1,Type=String,Description="Variant identifier as specified in the variant catalog">
51
49
  ##INFO=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification (samples).">
52
50
  ##INFO=<ID=phyloP,Number=.,Type=String,Description="[PATH]/hg38.phyloP100way.bw">
53
- ##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance, based on '<PATH>/vip/v7.9.0/resources/inheritance_20240115.tsv' .
54
- ##InheritanceModesGene=List of inheritance modes for the gene, based on '<PATH>/vip/v7.9.0/resources/inheritance_20240115.tsv'
51
+ ##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance, based on '/<PATH_TO>/resources/inheritance_20250411.tsv' .
52
+ ##InheritanceModesGene=List of inheritance modes for the gene, based on '/<PATH_TO>/resources/inheritance_20250411.tsv'
55
53
  ##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.
56
54
  ##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
57
55
  ##SpliceAI_pred_DP_AL=SpliceAI predicted effect on splicing. Delta position for acceptor loss
@@ -62,215 +60,45 @@
62
60
  ##SpliceAI_pred_DS_DG=SpliceAI predicted effect on splicing. Delta score for donor gain
63
61
  ##SpliceAI_pred_DS_DL=SpliceAI predicted effect on splicing. Delta score for donor loss
64
62
  ##SpliceAI_pred_SYMBOL=SpliceAI gene symbol
65
- ##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'
66
- ##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"
63
+ ##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]/hmtvar_trna_scores.tsv.gz --polyphen s --pubmed --refseq --safe --shift_3prime --sift s --symbol --total_length --use_given_ref --vcf'
64
+ ##VEP="v111" time="2026-02-05 13:42:14" cache="/<PATH_TO>/resources/vep/cache/homo_sapiens_refseq/111_GRCh38" ensembl-io=111.dbba8d6 ensembl-variation=111.d616b1e 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"
67
65
  ##VIPC=VIP decision tree classification
68
66
  ##VIPP=VIP decision tree path (ampersand separated)
69
- ##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
70
- ##VIP_treeVersion=4.1.1
71
- ##VKGL=file:<PATH>/vip/v7.9.0/resources/GRCh38/vkgl_consensus_20240401.tsv'
67
+ ##VIP_treeCommand=--input vip_annotated.vcf.gz_replaced.vcf.gz --metadata /<PATH_TO>/vip/resources/field_metadata.json --config /<PATH_TO>/vip/resources/decision_tree_GRCh38.json --path --output vip_classified.vcf.gz_replaced.vcf.gz
68
+ ##VIP_treeVersion=6.0.0
69
+ ##VKGL=file:/<PATH_TO>/resources/GRCh38/vkgl_consensus_20250701.tsv'
72
70
  ##VKGL_CL=VKGL consensus variant classification.
73
- ##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
74
- ##bcftools_viewVersion=1.17+htslib-1.17
71
+ ##apogee_Score=Score assigned by APOGEE
72
+ ##apogee_Uscore=Unbiased score assigned by APOGEE
75
73
  ##clinVar_CLNID=ClinVar variation identifier
76
74
  ##clinVar_CLNREVSTAT=ClinVar review status for the Variation ID
77
75
  ##clinVar_CLNSIG=Clinical significance for this single variant; multiple values are separated by a vertical bar
78
76
  ##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
79
77
  ##contig=<ID=chr1,length=248956422>
78
+ ##contig=<ID=chr2,length=242193529>
79
+ ##contig=<ID=chr3,length=198295559>
80
+ ##contig=<ID=chr4,length=190214555>
81
+ ##contig=<ID=chr5,length=181538259>
82
+ ##contig=<ID=chr6,length=170805979>
83
+ ##contig=<ID=chr7,length=159345973>
84
+ ##contig=<ID=chr8,length=145138636>
85
+ ##contig=<ID=chr9,length=138394717>
80
86
  ##contig=<ID=chr10,length=133797422>
81
87
  ##contig=<ID=chr11,length=135086622>
82
- ##contig=<ID=chr11_KI270721v1_random,length=100316>
83
88
  ##contig=<ID=chr12,length=133275309>
84
89
  ##contig=<ID=chr13,length=114364328>
85
90
  ##contig=<ID=chr14,length=107043718>
86
- ##contig=<ID=chr14_GL000009v2_random,length=201709>
87
- ##contig=<ID=chr14_GL000194v1_random,length=191469>
88
- ##contig=<ID=chr14_GL000225v1_random,length=211173>
89
- ##contig=<ID=chr14_KI270722v1_random,length=194050>
90
- ##contig=<ID=chr14_KI270723v1_random,length=38115>
91
- ##contig=<ID=chr14_KI270724v1_random,length=39555>
92
- ##contig=<ID=chr14_KI270725v1_random,length=172810>
93
- ##contig=<ID=chr14_KI270726v1_random,length=43739>
94
91
  ##contig=<ID=chr15,length=101991189>
95
- ##contig=<ID=chr15_KI270727v1_random,length=448248>
96
92
  ##contig=<ID=chr16,length=90338345>
97
- ##contig=<ID=chr16_KI270728v1_random,length=1872759>
98
93
  ##contig=<ID=chr17,length=83257441>
99
- ##contig=<ID=chr17_GL000205v2_random,length=185591>
100
- ##contig=<ID=chr17_KI270729v1_random,length=280839>
101
- ##contig=<ID=chr17_KI270730v1_random,length=112551>
102
94
  ##contig=<ID=chr18,length=80373285>
103
95
  ##contig=<ID=chr19,length=58617616>
104
- ##contig=<ID=chr1_KI270706v1_random,length=175055>
105
- ##contig=<ID=chr1_KI270707v1_random,length=32032>
106
- ##contig=<ID=chr1_KI270708v1_random,length=127682>
107
- ##contig=<ID=chr1_KI270709v1_random,length=66860>
108
- ##contig=<ID=chr1_KI270710v1_random,length=40176>
109
- ##contig=<ID=chr1_KI270711v1_random,length=42210>
110
- ##contig=<ID=chr1_KI270712v1_random,length=176043>
111
- ##contig=<ID=chr1_KI270713v1_random,length=40745>
112
- ##contig=<ID=chr1_KI270714v1_random,length=41717>
113
- ##contig=<ID=chr2,length=242193529>
114
96
  ##contig=<ID=chr20,length=64444167>
115
97
  ##contig=<ID=chr21,length=46709983>
116
98
  ##contig=<ID=chr22,length=50818468>
117
- ##contig=<ID=chr22_KI270731v1_random,length=150754>
118
- ##contig=<ID=chr22_KI270732v1_random,length=41543>
119
- ##contig=<ID=chr22_KI270733v1_random,length=179772>
120
- ##contig=<ID=chr22_KI270734v1_random,length=165050>
121
- ##contig=<ID=chr22_KI270735v1_random,length=42811>
122
- ##contig=<ID=chr22_KI270736v1_random,length=181920>
123
- ##contig=<ID=chr22_KI270737v1_random,length=103838>
124
- ##contig=<ID=chr22_KI270738v1_random,length=99375>
125
- ##contig=<ID=chr22_KI270739v1_random,length=73985>
126
- ##contig=<ID=chr2_KI270715v1_random,length=161471>
127
- ##contig=<ID=chr2_KI270716v1_random,length=153799>
128
- ##contig=<ID=chr3,length=198295559>
129
- ##contig=<ID=chr3_GL000221v1_random,length=155397>
130
- ##contig=<ID=chr4,length=190214555>
131
- ##contig=<ID=chr4_GL000008v2_random,length=209709>
132
- ##contig=<ID=chr5,length=181538259>
133
- ##contig=<ID=chr5_GL000208v1_random,length=92689>
134
- ##contig=<ID=chr6,length=170805979>
135
- ##contig=<ID=chr7,length=159345973>
136
- ##contig=<ID=chr8,length=145138636>
137
- ##contig=<ID=chr9,length=138394717>
138
- ##contig=<ID=chr9_KI270717v1_random,length=40062>
139
- ##contig=<ID=chr9_KI270718v1_random,length=38054>
140
- ##contig=<ID=chr9_KI270719v1_random,length=176845>
141
- ##contig=<ID=chr9_KI270720v1_random,length=39050>
142
- ##contig=<ID=chrEBV,length=171823>
143
- ##contig=<ID=chrM,length=16569>
144
- ##contig=<ID=chrUn_GL000195v1,length=182896>
145
- ##contig=<ID=chrUn_GL000213v1,length=164239>
146
- ##contig=<ID=chrUn_GL000214v1,length=137718>
147
- ##contig=<ID=chrUn_GL000216v2,length=176608>
148
- ##contig=<ID=chrUn_GL000218v1,length=161147>
149
- ##contig=<ID=chrUn_GL000219v1,length=179198>
150
- ##contig=<ID=chrUn_GL000220v1,length=161802>
151
- ##contig=<ID=chrUn_GL000224v1,length=179693>
152
- ##contig=<ID=chrUn_GL000226v1,length=15008>
153
- ##contig=<ID=chrUn_KI270302v1,length=2274>
154
- ##contig=<ID=chrUn_KI270303v1,length=1942>
155
- ##contig=<ID=chrUn_KI270304v1,length=2165>
156
- ##contig=<ID=chrUn_KI270305v1,length=1472>
157
- ##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
- ##contig=<ID=chrUn_KI270316v1,length=1444>
162
- ##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
- ##contig=<ID=chrUn_KI270412v1,length=1179>
204
- ##contig=<ID=chrUn_KI270414v1,length=2489>
205
- ##contig=<ID=chrUn_KI270417v1,length=2043>
206
- ##contig=<ID=chrUn_KI270418v1,length=2145>
207
- ##contig=<ID=chrUn_KI270419v1,length=1029>
208
- ##contig=<ID=chrUn_KI270420v1,length=2321>
209
- ##contig=<ID=chrUn_KI270422v1,length=1445>
210
- ##contig=<ID=chrUn_KI270423v1,length=981>
211
- ##contig=<ID=chrUn_KI270424v1,length=2140>
212
- ##contig=<ID=chrUn_KI270425v1,length=1884>
213
- ##contig=<ID=chrUn_KI270429v1,length=1361>
214
- ##contig=<ID=chrUn_KI270435v1,length=92983>
215
- ##contig=<ID=chrUn_KI270438v1,length=112505>
216
- ##contig=<ID=chrUn_KI270442v1,length=392061>
217
- ##contig=<ID=chrUn_KI270448v1,length=7992>
218
- ##contig=<ID=chrUn_KI270465v1,length=1774>
219
- ##contig=<ID=chrUn_KI270466v1,length=1233>
220
- ##contig=<ID=chrUn_KI270467v1,length=3920>
221
- ##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
- ##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>
231
- ##contig=<ID=chrUn_KI270518v1,length=2186>
232
- ##contig=<ID=chrUn_KI270519v1,length=138126>
233
- ##contig=<ID=chrUn_KI270521v1,length=7642>
234
- ##contig=<ID=chrUn_KI270522v1,length=5674>
235
- ##contig=<ID=chrUn_KI270528v1,length=2983>
236
- ##contig=<ID=chrUn_KI270529v1,length=1899>
237
- ##contig=<ID=chrUn_KI270530v1,length=2168>
238
- ##contig=<ID=chrUn_KI270538v1,length=91309>
239
- ##contig=<ID=chrUn_KI270539v1,length=993>
240
- ##contig=<ID=chrUn_KI270544v1,length=1202>
241
- ##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
- ##contig=<ID=chrUn_KI270583v1,length=1400>
247
- ##contig=<ID=chrUn_KI270584v1,length=4513>
248
- ##contig=<ID=chrUn_KI270587v1,length=2969>
249
- ##contig=<ID=chrUn_KI270588v1,length=6158>
250
- ##contig=<ID=chrUn_KI270589v1,length=44474>
251
- ##contig=<ID=chrUn_KI270590v1,length=4685>
252
- ##contig=<ID=chrUn_KI270591v1,length=5796>
253
- ##contig=<ID=chrUn_KI270593v1,length=3041>
254
- ##contig=<ID=chrUn_KI270741v1,length=157432>
255
- ##contig=<ID=chrUn_KI270742v1,length=186739>
256
- ##contig=<ID=chrUn_KI270743v1,length=210658>
257
- ##contig=<ID=chrUn_KI270744v1,length=168472>
258
- ##contig=<ID=chrUn_KI270745v1,length=41891>
259
- ##contig=<ID=chrUn_KI270746v1,length=66486>
260
- ##contig=<ID=chrUn_KI270747v1,length=198735>
261
- ##contig=<ID=chrUn_KI270748v1,length=93321>
262
- ##contig=<ID=chrUn_KI270749v1,length=158759>
263
- ##contig=<ID=chrUn_KI270750v1,length=148850>
264
- ##contig=<ID=chrUn_KI270751v1,length=150742>
265
- ##contig=<ID=chrUn_KI270752v1,length=27745>
266
- ##contig=<ID=chrUn_KI270753v1,length=62944>
267
- ##contig=<ID=chrUn_KI270754v1,length=40191>
268
- ##contig=<ID=chrUn_KI270755v1,length=36723>
269
- ##contig=<ID=chrUn_KI270756v1,length=79590>
270
- ##contig=<ID=chrUn_KI270757v1,length=71251>
271
99
  ##contig=<ID=chrX,length=156040895>
272
100
  ##contig=<ID=chrY,length=57227415>
273
- ##contig=<ID=chrY_KI270740v1_random,length=37240>
101
+ ##contig=<ID=chrM,length=16569>
274
102
  ##existing_InFrame_oORFs=The number of existing inFrame overlapping ORFs (inFrame oORF) at the 5 prime UTR
275
103
  ##existing_OutOfFrame_oORFs=The number of existing out-of-frame overlapping ORFs (OutOfFrame oORF) at the 5 prime UTR
276
104
  ##existing_uORFs=The number of existing uORFs with a stop codon within the 5 prime UTR
@@ -283,39 +111,44 @@
283
111
  ##gnomAD_HN=gnomAD number of homozygotes
284
112
  ##gnomAD_QC=gnomAD quality control filters that failed
285
113
  ##gnomAD_SRC=gnomAD source: E=exomes, G=genomes, T=total
114
+ ##hmtvar_DiseaseScore=Disease score assigned by HmtVar
115
+ ##mitoTip_Quartile=MitoTip Quartile
116
+ ##mitoTip_Score=MitoTip Score
286
117
  ##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
118
  ##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
119
+ ##VIP_Version=9.0.0
120
+ ##VIP_Command=/<PATH_TO>/nextflow-25.10.2-dist -C /<PATH_TO>/vip/config/nxf_cram.config,/<PATH_TO>/vip/test/suites/cram/resources/nanopore_duo.cfg -log /<PATH_TO>/vip/test/output/cram/nanopore_duo/.nxf.log run /<PATH_TO>/vip/vip_cram.nf -offline -profile slurm -with-report /<PATH_TO>/vip/test/output/cram/nanopore_duo/nxf_report.html -with-timeline /<PATH_TO>/vip/test/output/cram/nanopore_duo/nxf_timeline.html --input /<PATH_TO>/vip/test/output/cram/nanopore_duo/samplesheet.tsv --output /<PATH_TO>/vip/test/output/cram/nanopore_duo -resume
292
121
  #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
122
+ 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;Disease=NIID;DisplayRU=CGG;END=149390841;HGNCId=53924;InheritanceMode=AD;REPID=NOTCH2NLC;RU_CAT=GGC;RankScore=1:10;STR_NORMAL_MAX=38;STR_PATHOLOGIC_MIN=66;STR_STATUS=normal;SVTYPE=STR;Source=GeneReviews;SourceDisplay=GeneReviews_Internet_2019-11-07;SourceId=NBK535148;VIPC_S=U2 GT:AD:LC:RU_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:33:33:GGC:13.6-17.4:1:18:GGC(20),CGCGCTGCTGTG(11),AAC(1),GCTCAGCTGTCGGCGCGCTGCTG(1):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
123
+ 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_CAT=GCA;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:51:51:GCA:12.6-13.4:1:13:GCA(30),AGCCTCAGTGCGG(21):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
124
+ 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_CAT=GCA;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:54:54:GCA:11.1-12.1:1:12:GCCGCGCCGAGCAGCGGCCGCG(2),GGC(1),GCCGCG(1),GCAGCAGCCGCCGCCACCGCAGCCACGGC(1),GCAGCCGCC(1),GCA(39),CAGCCGCCA(1),GCCGCGGCCGCCGGCAGCG(1),GCC(2),GCCGCGCCGCCCCGCGGCGGCGGCGGCAGCAGCAGCG(1),GCGGCCGCGGCCGCCCGGCAGCA(3),CCGCCACCG(1):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
125
+ 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_CAT=GCC;SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:54:54:GCA:5.6-6.5:0:6:GCAGCAGCCGCCGCCACCGCAGCCACGGC(1),GCA(42),CCGCGCCGCCCCGCGGCGGCGGCGGCAGCAGCAGCGG(1),GCC(6),GCGGCCGCGGCCGCCCGGCAGCA(3),CGCCGGCAGCGGCCGCGGC(1):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
126
+ 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_CAT=CAGG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:57:57:CAGA:15.3-16.0:0:16:CAGG(2),CAGA(55):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
127
+ 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_CAT=CAGA;SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:57:57:CAGA:5.7-6.4:1:6:CAGG(3),CAGA(54):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
128
+ 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_CAT=CA;SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:57:57:CA:12.1-13.8:1:14:CA(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
129
+ 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_CAT=AARRG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:29,23:52:AAAAG:112.6-114.6,11.7-12.1:1:114,12:AAAAG(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
130
+ 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_CAT=GCN;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:62:62:GCTGCCGCC:6.0-6.4:0:6:GCCGCCGCTGCCGCGGCCGCC(2),GCTGCCGCC(54),GCCGCA(1),CCGCCGCCC(1),GCC_GCCGCCGCTGCCGCGCCGCC(4):62:AR,AD:8929:U2:gt&gq&only_IP&vig&vim&exit_u2
131
+ 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_CAT=GCT;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:40:40:GCT:9.9-10.5:1:10:GCGCGCACCCCC(1),GCTGCTGCAGGAGGCGAGGCG(1),AGCTGGCGGGG(1),GGAGCTGGCAG(1),GCT_GGGAGCTGGGCA(1),GCT(30),GCTGGAGGCG(1),CGCGCGCACTCACA(1),AGCTGGCAGGG(2),CGCACT(1):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
132
+ 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_CAT=TGC;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:40:40:TGC:30.3-30.8:1:31:TGC(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
133
+ 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_CAT=GCA;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:40:40:GCA:35.9-36.5:1:36:GCA(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
134
+ 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_CAT=A;SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:35:35:AAAAAAGA:3.9-4.5:0:4:TACAAAAAAA(2),AAAATAAAGAAAGAAGAAG(1),AAAAGAAGA(2),AAAAAAAAGAAAAGAAG(1),AAAAAAGA(27),AAG(1),AAAAAAAAGAAAAAGAAAG_AAAAAG(1):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
135
+ 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_CAT=GAA;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:35:35:AAAAAAGA:3.6-4.9:0:4:TACAAAAAAA(2),AAAAAAGA(27),GAA(5),AAAAAAAAGAAAAAGAAAG_AAAAAG(1):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
136
+ 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_CAT=CAG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:49:49:CAG:17.5-18.3:1:18:CAG(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
137
+ 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_CAT=GCT;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:32,31:63:GCT:29.9-30.5,21.7-22.3:1:30,22:GCT(63):32,31:AR,AD:0.507937:6311: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
138
+ 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_CAT=CTA;SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:40:40:CTG:9.5-10.4:0:10:CTA(1),CTG(38),TCTATTTA(1):40:AR,AD,AR_C:chr13_70139384_C_:6315:U2:gt&gq&only_IP&vig&vim&exit_u2
139
+ 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_CAT=CTG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:40:40:CTG:14.3-15.3:1:15:TAC(1),CTG(38),TCTATTTA(1):40:AR,AD,AR_C:chr13_70139354_C_:6315:U2:gt&gq&only_IP&vig&vim&exit_u2
140
+ 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_CAT=GCG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:44:44:GCG:5.9-6.5:1:6:GGGCGGCGGGCCCCAGTCAGAGCGGGCGATGCGGGCGGGGC(1),GCGGGGGCT(1),GCG(42):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
141
+ 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_CAT=GCT;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:50:50:CTG:20.9-22.2:1:22:CTG(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
142
+ 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_CAT=GCG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:39:39:GCG:10.3-11.8:1:13:GCAGCGGCG_GGGC(1),GCG(37),GGCGCGGCGCGCA(1):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
143
+ 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_CAT=CTG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:37:37:CTG:15.7-16.4:1:16:CTG(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
144
+ 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_CAT=CAG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:29,25:54:CAG:31.6-32.3,12.7-13.9:1:32,13:GGA(1),GAGGAGAGGAGGAGCAG(1),CAG(52):29,25:AR,AD:0.537037:6925: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
145
+ 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_CAT=CTG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:63:63:CTG:10.5-11.2:1:11:CTG(62),TGGCCCGCC(1):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
146
+ 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_CAT=CCG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:20,38:58:CCG:15.7-15.7,11.3-12.6:1:16,11:CCGCCGCAGCCTCCGCCTCC(1),CCG(57):20,38:AR,AD:0.344828:10755: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
147
+ 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_CAT=CAG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:40:40:CAG:10.7-11.3:1:11:CAG(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
148
+ 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_CAT=GGCCTG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:48:48:GGCCTG:5.5-6.1:1:5:GGCCTG(47),GGCCTGCGCCGGGCCTGAGACAGAGCCTG(1):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
149
+ 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_CAT=CGCCTG;SVTYPE=STR;VIPC_S=U2 GT:AD:LC:RU_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIC:VIG:VIPC_S:VIPP_S 1/1:48:48:CGCCTG:4.6-5.5:1:4:GCCT_GCCTGCCT(1),GGCCTGCGCCGGGCCTGAGACAGAGCCTG(1),CGCCTG(46):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
150
+ 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_CAT=CGCGGGGCGGGG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1/1:43:43:CGCGGGGCGGGG:2.3-2.6:1:3:GGGCG_GGGCGG_GGGCGGG(1),GCGCAGGGGCGGG_GCGCGGG(1),GCGCGGGGGGCGGGG(1),CGCGGGGCGGGG(36),GCGCGGG_GCGGG(1),GGGACGCGC(1),GCGGGGAC(1),GGGCGGGGAGCC_GGGGCGC(1):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
151
+ 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_CAT=ATTCT;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIAB:VIG:VIPC_S:VIPP_S 1/2:18,25:43:ATTCT:15.9-16.1,11.2-11.9:1:16,12:ATTCT(42),ATTCTATTCTATTTTATCTTCATTTC(1):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
152
+ 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_CAT=GCA;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1:18:18:GCA:26.2-27.4:1:27:GCA(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
153
+ 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_CAT=CGG;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1:30:30:CGG:30.5-31.4:1:31:CGG(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
154
+ 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_CAT=GCC;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_CALL:RU_CI:RU_MATCH:RU_NR:RU_SEEN:RU_SPAN:VI:VIG:VIPC_S:VIPP_S 1:26:26:GCC:18.4-19.1:1:19:GCC(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