@molgenis/vip-report-template 7.1.2 → 8.0.0

package/src/mocks/GRCh38/vcf/family.vcf

@@ -0,0 +1,312 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##ALPHSCORE=AlphScore_final scores as described in https://doi.org/10.1093/bioinformatics/btad280
+##ASV_ACMG_class=AnnotSv 'ACMG_class' output.
+##ASV_AnnotSV_ranking_criteria=AnnotSv 'AnnotSV_ranking_criteria' output.
+##ASV_AnnotSV_ranking_score=AnnotSv 'AnnotSV_ranking_score' output.
+##ASV_Gene_name=AnnotSv 'Gene_name' output.
+##ASV_RE_gene=AnnotSv 'RE_gene' output.
+##CAPICE_CL=CAPICE classification
+##CAPICE_SC=CAPICE score
+##FATHMM_MKL_NC=FATHMM_MKL_NC: Predict the Functional Consequences of Non-Coding Single Nucleotide Variants (SNVs)
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##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">
+##FORMAT=<ID=VIAB,Number=1,Type=Float,Description="VIP calculated allele balance">
+##FORMAT=<ID=VIC,Number=1,Type=String,Description="Possible Compound hetrozygote variants.">
+##FORMAT=<ID=VID,Number=1,Type=Integer,Description="De novo variant.">
+##FORMAT=<ID=VIG,Number=.,Type=String,Description="Genes with a (potential) inheritance match.">
+##FORMAT=<ID=VIM,Number=1,Type=Integer,Description="Inheritance Match: Genotypes, affected statuses and known gene inheritance patterns match.">
+##FORMAT=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
+##FORMAT=<ID=VIPP_S,Number=.,Type=String,Description="VIP decision tree path.">
+##Grantham=Grantham Matrix score - Grantham, R. Amino Acid Difference Formula to Help Explain Protein Evolution, Science 1974 Sep 6;185(4154):862-4.
+##HPO=List of HPO terms for the gene
+##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
+##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|phyloP|VIPC|VIPP">
+##INFO=<ID=Disease,Number=1,Type=String,Description="Associated disorder">
+##INFO=<ID=DisplayRU,Number=1,Type=String,Description="Display repeat unit familiar to clinician">
+##INFO=<ID=HGNCId,Number=1,Type=Integer,Description="HGNC gene id for associated disease gene">
+##INFO=<ID=InheritanceMode,Number=1,Type=String,Description="Main mode of inheritance for disorder">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
+##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
+##INFO=<ID=OLD_REC,Number=1,Type=String,Description="Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX">
+##INFO=<ID=RankScore,Number=1,Type=String,Description="RankScore for variant in this family as family(str):score(int)">
+##INFO=<ID=ReverseComplementedAlleles,Number=0,Type=Flag,Description="The REF and the ALT alleles have been reverse complemented in liftover since the mapping from the previous reference to the current one was on the negative strand.">
+##INFO=<ID=STR_NORMAL_MAX,Number=1,Type=Integer,Description="Max number of repeats allowed to call as normal">
+##INFO=<ID=STR_PATHOLOGIC_MIN,Number=1,Type=Integer,Description="Min number of repeats required to call as pathologic">
+##INFO=<ID=STR_STATUS,Number=A,Type=String,Description="Repeat expansion status. Alternatives in [normal, pre_mutation, full_mutation]">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=Source,Number=1,Type=String,Description="Source collection for variant definition">
+##INFO=<ID=SourceDisplay,Number=1,Type=String,Description="Source for variant definition, display">
+##INFO=<ID=SourceId,Number=1,Type=String,Description="Source id for variant definition">
+##INFO=<ID=SwappedAlleles,Number=0,Type=Flag,Description="The REF and the ALT alleles have been swapped in liftover due to changes in the reference. It is possible that not all INFO annotations reflect this swap, and in the genotypes, only the GT, PL, and AD fields have been modified. You should check the TAGS_TO_REVERSE parameter that was used during the LiftOver to be sure.">
+##INFO=<ID=SweGenMean,Number=1,Type=Float,Description="Average number of repeat unit copies in population">
+##INFO=<ID=SweGenStd,Number=1,Type=Float,Description="Standard deviation of number of repeat unit copies in population">
+##INFO=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
+##INFO=<ID=gnomAD,Number=.,Type=String,Description="/groups/solve-rd/tmp10/vip/resources/GRCh38/gnomad.genomes.v3.1.2.sites.stripped.vcf.gz (exact)">
+##INFO=<ID=gnomAD_AF,Number=.,Type=String,Description="AF field from /groups/solve-rd/tmp10/vip/resources/GRCh38/gnomad.genomes.v3.1.2.sites.stripped.vcf.gz">
+##INFO=<ID=gnomAD_HN,Number=.,Type=String,Description="HN field from /groups/solve-rd/tmp10/vip/resources/GRCh38/gnomad.genomes.v3.1.2.sites.stripped.vcf.gz">
+##INFO=<ID=n_object0,Number=.,Type=String,Description="Annotations from Object test. Format: n_string1|n_string2|n_array1">
+##INFO=<ID=phyloP,Number=.,Type=String,Description="[PATH]/hg38.phyloP100way.bw">
+##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance.
+##InheritanceModesGene=List of inheritance modes for the gene
+##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.
+##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
+##SpliceAI_pred_DP_AL=SpliceAI predicted effect on splicing. Delta position for acceptor loss
+##SpliceAI_pred_DP_DG=SpliceAI predicted effect on splicing. Delta position for donor gain
+##SpliceAI_pred_DP_DL=SpliceAI predicted effect on splicing. Delta position for donor loss
+##SpliceAI_pred_DS_AG=SpliceAI predicted effect on splicing. Delta score for acceptor gain
+##SpliceAI_pred_DS_AL=SpliceAI predicted effect on splicing. Delta score for acceptor loss
+##SpliceAI_pred_DS_DG=SpliceAI predicted effect on splicing. Delta score for donor gain
+##SpliceAI_pred_DS_DL=SpliceAI predicted effect on splicing. Delta score for donor loss
+##SpliceAI_pred_SYMBOL=SpliceAI gene symbol
+##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]/ReMM.v0.4.hg38.tsv.gz --polyphen s --pubmed --refseq --safe --shift_3prime --sift s --symbol --total_length --use_given_ref --vcf'
+##VEP="v111" time="2025-11-04 09:47:27" cache="/apps/data/vip/resources/vep/cache/homo_sapiens_refseq/111_GRCh38" ensembl-funcgen=111.5327cdd ensembl=111.a6cc543 ensembl-io=111.dbba8d6 ensembl-variation=111.d616b1e 1000genomes="phase3" COSMIC="98" ClinVar="202306" HGMD-PUBLIC="20204" assembly="GRCh38.p14" dbSNP="156" gencode="GENCODE 45" genebuild="2014-07" gnomADe="r2.1.1" gnomADg="v3.1.2" polyphen="2.2.3" refseq="GCF_000001405.40-RS_2023_03 - GCF_000001405.40_GRCh38.p14_genomic.gff" regbuild="1.0" sift="6.2.1"
+##VIPC=VIP decision tree classification
+##VIPL=VIP decision tree labels (ampersand separated)
+##VIPP=VIP decision tree path (ampersand separated)
+##VIP_Command=nextflow run ./main.nf --input /groups/solve-rd/tmp10/testdata/testdata_b38.vcf --output /groups/solve-rd/tmp10/testdata_out/ --keep --pedigree /groups/solve-rd/tmp10/example.ped --probands Patient --phenotypes 'HP:0000951' --assembly GRCh38
+##VIP_Version=4.0.1
+##VIP_treeCommand=--input testdata_b38_chunk0_annotated.vcf.gz --config /groups/solve-rd/tmp10/vip/resources/decision_tree.json --labels 0 --path 0 --output testdata_b38_chunk0_classified.vcf.gz
+##VIP_treeVersion=2.2.0
+##VKGL=file:/apps/data/vip/resources/GRCh38/vkgl_consensus_20250401.tsv'
+##VKGL_CL=VKGL consensus variant classification.
+##clinVar_CLNID=ClinVar variation identifier
+##clinVar_CLNREVSTAT=ClinVar review status for the Variation ID
+##clinVar_CLNSIG=Clinical significance for this single variant; multiple values are separated by a vertical bar
+##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
+##contig=<ID=chr1,length=248956422>
+##contig=<ID=chr2,length=242193529>
+##contig=<ID=chr3,length=198295559>
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+##contig=<ID=chr5,length=181538259>
+##contig=<ID=chr6,length=170805979>
+##contig=<ID=chr7,length=159345973>
+##contig=<ID=chr8,length=145138636>
+##contig=<ID=chr9,length=138394717>
+##contig=<ID=chr10,length=133797422>
+##contig=<ID=chr11,length=135086622>
+##contig=<ID=chr12,length=133275309>
+##contig=<ID=chr13,length=114364328>
+##contig=<ID=chr14,length=107043718>
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+##contig=<ID=chrUn_KI270751v1,length=150742>
+##contig=<ID=chrUn_KI270752v1,length=27745>
+##contig=<ID=chrUn_KI270753v1,length=62944>
+##contig=<ID=chrUn_KI270754v1,length=40191>
+##contig=<ID=chrUn_KI270755v1,length=36723>
+##contig=<ID=chrUn_KI270756v1,length=79590>
+##contig=<ID=chrUn_KI270757v1,length=71251>
+##contig=<ID=chrUn_GL000214v1,length=137718>
+##contig=<ID=chrUn_KI270742v1,length=186739>
+##contig=<ID=chrUn_GL000216v2,length=176608>
+##contig=<ID=chrUn_GL000218v1,length=161147>
+##contig=<ID=chrEBV,length=171823>
+##existing_InFrame_oORFs=The number of existing inFrame overlapping ORFs (inFrame oORF) at the 5 prime UTR
+##existing_OutOfFrame_oORFs=The number of existing out-of-frame overlapping ORFs (OutOfFrame oORF) at the 5 prime UTR
+##existing_uORFs=The number of existing uORFs with a stop codon within the 5 prime UTR
+##fileDate=20200320
+##five_prime_UTR_variant_annotation=Output the annotation of a given 5 prime UTR variant
+##five_prime_UTR_variant_consequence=Output the variant consequences of a given 5 prime UTR variant: uAUG_gained, uAUG_lost, uSTOP_lost or uFrameshift
+##gnomAD_AF=gnomAD allele frequency
+##gnomAD_COV=gnomAD coverage (percent of individuals in gnomAD source)
+##gnomAD_FAF95=gnomAD filtering allele frequency (95% confidence)
+##gnomAD_FAF99=gnomAD filtering allele frequency (99% confidence)
+##gnomAD_HN=gnomAD number of homozygotes
+##gnomAD_QC=gnomAD quality control filters that failed
+##gnomAD_SRC=gnomAD source: E=exomes, G=genomes, T=total
+##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.
+##reference=/vip/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance">
+##VIP_Version=8.4.5
+##VIP_Command=/apps/data/vip/nextflow-24.10.6-dist -C /apps/software/vip/v8.4.5/config/nxf_vcf.config,/groups/umcg-gcc/tmp02/projects/vipt/umcg-bcharbon/testdata/extra.cfg -log /groups/umcg-gcc/tmp02/projects/vipt/umcg-bcharbon/testdata/./out/.nxf.log run /apps/software/vip/v8.4.5/vip_vcf.nf -offline -profile slurm -with-report /groups/umcg-gcc/tmp02/projects/vipt/umcg-bcharbon/testdata/./out/nxf_report.html -with-timeline /groups/umcg-gcc/tmp02/projects/vipt/umcg-bcharbon/testdata/./out/nxf_timeline.html --input /groups/umcg-gcc/tmp02/projects/vipt/umcg-bcharbon/testdata/./samplesheet.tsv --output /groups/umcg-gcc/tmp02/projects/vipt/umcg-bcharbon/testdata/./out
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Unrelated	Sister	Nephew	MotherHasQuiteALongName	Father	Patient
+chr1	9982480	HOM_REF	C	T	.	PASS	CSQ=T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_001297778.1|protein_coding|5/5||NM_001297778.1:c.619C>T|NP_001284707.1:p.Arg207Trp|778/3796|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1|||EntrezGene|||||0.06|0.079||pathogenic|0&1|1&1||||||||101|0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.23609488|||||||AR||LP|2.41641e-05|0.999777|1.809e-05|1.589e-05|0||T|37133|criteria_provided&_multiple_submitters&_no_conflicts|Pathogenic|||||||0.784|98.592|0.98061|0.17873|4.05700016021729|LP|filter&vkgl&exit_lp,T|downstream_gene_variant|MODIFIER|NMNAT1|64802|Transcript|NM_001297779.2|protein_coding||||||||||rs142968179&CM127756|1|714|1|||EntrezGene||||||||pathogenic|0&1|1&1|||||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.04292168|||||||AR||LP|2.41641e-05|0.999777|1.809e-05|1.589e-05|0||T|37133|criteria_provided&_multiple_submitters&_no_conflicts|Pathogenic||||||||98.592|0.98061|0.17873|4.05700016021729|LP|filter&vkgl&exit_lp,T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_022787.4|protein_coding|5/5||NM_022787.4:c.619C>T|NP_073624.2:p.Arg207Trp|716/3734|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|EntrezGene|||||0.06|0.079||pathogenic|0&1|1&1||||||||101|0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.269153|||||||AR||LP|2.41641e-05|0.999777|1.809e-05|1.589e-05|0||T|37133|criteria_provided&_multiple_submitters&_no_conflicts|Pathogenic|||||||0.784|98.592|0.98061|0.17873|4.05700016021729|LP|filter&vkgl&exit_lp;ReverseComplementedAlleles;VIPC_S=U2;n_object0=dummy5|c|1&2,dummy7||1&2,dummy1|d|1&2,dummy4|b|1&2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|.:50:50:.:.:.:.	./.:10:50:.:.:.:.	1|0:50:50:1:0:U2,U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr2	47408528	symbolic2	G	<INS>	.	PASS	CSQ=insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_000251.3|protein_coding|2-8/16|2-8/15|||376-?/3115|340-?/2805|114-?/934||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001258281.1|protein_coding|3-9/17|3-9/16|||281-?/3025|142-?/2607|48-?/868||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406631.1|protein_coding|2-8/18|2-8/17|||376-?/3210|340-?/2940|114-?/979||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406632.1|protein_coding|2-8/19|2-8/18|||376-?/3284|340-?/2931|114-?/976||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406633.1|protein_coding|2-8/19|2-8/18|||376-?/3134|340-?/2928|114-?/975||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406634.1|protein_coding|2-8/17|2-8/16|||376-?/5693|340-?/2925|114-?/974||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406635.1|protein_coding|2-8/21|2-8/20|||376-?/3060|340-?/2919|114-?/972||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406636.1|protein_coding|2-8/21|2-8/20|||376-?/3027|340-?/2886|114-?/961||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406637.1|protein_coding|2-8/17|2-8/16|||376-?/4436|340-?/2874|114-?/957||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406638.1|protein_coding|2-8/18|2-8/17|||376-?/10637|340-?/2844|114-?/947||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406639.1|protein_coding|2-8/18|2-8/17|||376-?/3191|340-?/2838|114-?/945||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406640.1|protein_coding|2-8/20|2-8/19|||376-?/3038|340-?/2844|114-?/947||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406641.1|protein_coding|2-8/17|2-8/16|||376-?/10598|340-?/2805|114-?/934||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406642.1|protein_coding|2-8/17|2-8/16|||376-?/2909|340-?/2790|114-?/929||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406643.1|protein_coding|2-8/17|2-8/16|||376-?/3626|340-?/2781|114-?/926||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406644.1|protein_coding|2-8/17|2-8/16|||376-?/5585|340-?/2775|114-?/924||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406645.1|protein_coding|2-8/16|2-8/15|||376-?/10404|340-?/2766|114-?/921||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406646.1|protein_coding|2-8/17|2-8/16|||376-?/4488|340-?/2757|114-?/918||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406647.1|protein_coding|2-7/17|2-7/16|||376-?/3065|340-?/2712|114-?/903||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406648.1|protein_coding|2-8/16|2-8/15|||376-?/2858|340-?/2658|114-?/885||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406649.1|protein_coding|2-7/16|2-7/15|||376-?/10448|340-?/2655|114-?/884||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406650.1|protein_coding|2-7/15|2-7/14|||376-?/2965|340-?/2655|114-?/884||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406651.1|protein_coding|2-7/16|2-7/15|||376-?/5435|340-?/2625|114-?/874||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406652.1|protein_coding|2-7/15|2-7/14|||376-?/10254|340-?/2616|114-?/871||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406653.1|protein_coding|2-8/15|2-8/14|||316-?/4160|280-?/2601|94-?/866||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&5_prime_UTR_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406654.1|protein_coding|2-8/16|2-8/15|||296-?/10324|-/2346|-/781||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406655.1|protein_coding|2-8/12|2-8/11|||376-?/2660|340-?/2040|114-?/679||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&5_prime_UTR_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406656.1|protein_coding|2-9/17|2-9/16|||376-?/10502|-/1869|-/622||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406657.1|protein_coding|2-8/11|2-8/10|||376-?/2562|340-?/1692|114-?/563||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&5_prime_UTR_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406658.1|protein_coding|2-8/16|2-8/15|||376-?/3077|-/1449|-/482||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&5_prime_UTR_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406659.1|protein_coding|2-9/17|2-9/16|||376-?/3227|-/1449|-/482||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&5_prime_UTR_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406660.1|protein_coding|2-11/19|2-11/18|||376-?/3424|-/1449|-/482||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&5_prime_UTR_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406661.1|protein_coding|2-10/18|2-10/17|||376-?/3379|-/1449|-/482||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&5_prime_UTR_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406662.1|protein_coding|2-10/18|2-10/17|||376-?/3296|-/1449|-/482||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|coding_sequence_variant&3_prime_UTR_variant&intron_variant|MODIFIER|MSH2|4436|Transcript|NM_001406666.1|protein_coding|2-9/9|2-8/8|||376-?/1589|340-?/1425|114-?/474||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&5_prime_UTR_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406669.1|protein_coding|2-9/17|2-9/16|||376-?/10516|-/1410|-/469||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|coding_sequence_variant&3_prime_UTR_variant&intron_variant|MODIFIER|MSH2|4436|Transcript|NM_001406672.1|protein_coding|2-8/8|2-7/7|||376-?/1439|340-?/1275|114-?/424||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&coding_sequence_variant&intron_variant|HIGH|MSH2|4436|Transcript|NM_001406674.1|protein_coding|2-8/18|2-8/17|||376-?/5813|340-?/3045|114-?/1014||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176230.1|misc_RNA|2-8/17|2-8/16|||376-?/6248||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176231.1|misc_RNA|2-8/17|2-8/16|||376-?/5553||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176232.1|misc_RNA|2-8/18|2-8/17|||376-?/3721||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176233.1|misc_RNA|2-7/17|2-7/16|||368-?/3563||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176234.1|misc_RNA|2-8/19|2-8/18|||376-?/3249||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176235.1|misc_RNA|2-8/20|2-8/19|||376-?/5158||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176236.1|misc_RNA|2-8/18|2-8/17|||376-?/4678||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176237.1|misc_RNA|2-8/19|2-8/18|||376-?/4872||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176238.1|misc_RNA|2-8/19|2-8/18|||376-?/4811||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176239.1|misc_RNA|2-8/18|2-8/17|||376-?/4682||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176240.1|misc_RNA|2-8/15|2-8/14|||376-?/10199||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176241.1|misc_RNA|2-8/21|2-8/20|||376-?/3300||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176242.1|misc_RNA|2-8/19|2-8/18|||376-?/3232||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176243.1|misc_RNA|2-7/19|2-7/18|||376-?/3096||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176244.1|misc_RNA|2-8/23|2-8/22|||376-?/3726||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176245.1|misc_RNA|2-8/19|2-8/18|||376-?/3182||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176246.1|misc_RNA|2-8/19|2-8/18|||376-?/3264||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176247.1|misc_RNA|2-8/20|2-8/19|||376-?/3208||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176248.1|misc_RNA|2-8/21|2-8/20|||376-?/3408||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176249.1|misc_RNA|2-9/16|2-9/15|||376-?/4450||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,insertion|feature_elongation&non_coding_transcript_exon_variant&intron_variant|HIGH|MSH2|4436|Transcript|NR_176250.1|misc_RNA|2-6/14|2-6/13|||376-?/2855||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||NA|||MSH2|||||||VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus;SVLEN=-49314;SVTYPE=INS;VIPC_S=U2;n_object0=dummy5|c|1&2,dummy7||1&2,dummy1|d|1&2,dummy4|b|1&2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0: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&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr4	105399137	.	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_006903.4|protein_coding|7/11||NM_006903.4:c.596C>T|NP_008834.3:p.Pro199Leu|616/1586|596/918|199/305|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.984||pathogenic&pathogenic/likely_pathogenic&likely_pathogenic|0&1&1|1&1&1||||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.68027097|||||||AR||LP|0.00034709|0.994082|0.00032286|0.0003137|0||T|372226|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic|||||||0.787|91.4276|0.99641|0.937643|9.48299980163574|LP|filter&vkgl&exit_lp,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176866.2|protein_coding|4/8||NM_176866.2:c.377C>T|NP_789842.2:p.Pro126Leu|397/1367|377/699|126/232|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.994||pathogenic&pathogenic/likely_pathogenic&likely_pathogenic|0&1&1|1&1&1||||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.6379048|||||||AR||LP|0.00034709|0.994082|0.00032286|0.0003137|0||T|372226|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic|||||||0.787|91.4276|0.99641|0.937643|9.48299980163574|LP|filter&vkgl&exit_lp,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176867.3|protein_coding|2/6||NM_176867.3:c.185C>T|NP_789843.2:p.Pro62Leu|205/1175|185/507|62/168|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.995||pathogenic&pathogenic/likely_pathogenic&likely_pathogenic|0&1&1|1&1&1||||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7167147|||||||AR||LP|0.00034709|0.994082|0.00032286|0.0003137|0||T|372226|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic|||||||0.787|91.4276|0.99641|0.937643|9.48299980163574|LP|filter&vkgl&exit_lp,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176869.3|protein_coding|8/12||NM_176869.3:c.683C>T|NP_789845.1:p.Pro228Leu|695/1665|683/1005|228/334|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1||1|EntrezGene|||||0|0.995||pathogenic&pathogenic/likely_pathogenic&likely_pathogenic|0&1&1|1&1&1||||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.66750205|||||||AR||LP|0.00034709|0.994082|0.00032286|0.0003137|0||T|372226|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic|||||||0.787|91.4276|0.99641|0.937643|9.48299980163574|LP|filter&vkgl&exit_lp,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001252884|enhancer||||||||||rs138215926&CM1610192&COSV58994362|1|||||||||||||pathogenic&pathogenic/likely_pathogenic&likely_pathogenic|0&1&1|1&1&1||||||||||||||||||VUS|0.86275065||||||||||0.00034709|0.994082|0.00032286|0.0003137|0||T|372226|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||91.4276|0.99641|0.937643|9.48299980163574|LP|filter&vkgl&clinVar&exit_lp;VIPC_S=U2;n_object0=dummy5|c|1&2,dummy7||1&2,dummy1|d|1&2,dummy4|b|1&2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2,U2,U2,U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr7	42025358	.	GACTC	G	.	PASS	CSQ=-|frameshift_variant|HIGH|GLI3|2737|Transcript|NM_000168.6|protein_coding|9/15||NM_000168.6:c.1258_1261del|NP_000159.3:p.Glu420LeufsTer3|1539-1542/8405|1258-1261/4743|420-421/1580|ES/X|GAGTct/ct||1||-1||1|EntrezGene|||||||||||||||||||18|21|-40|6|0.00|0.00|0.00|0.00|GLI3|VUS|0.9901833|||||||AD||LP||||||||||||||||||99.756||0.987456||LP|filter&vkgl&exit_lp;VIPC_S=U2;n_object0=dummy4|b|1&2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2:gt&gq&only_IP&vim&exit_u2
+chr8	60852584	breakend1	G	]11:134014225]G	.	PASS	BND_DEPTH=26;CSQ=]11:134014225]G|feature_truncation&intron_variant|HIGH|CHD7|55636|Transcript|NM_001316690.1|protein_coding||2/4|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||NA|||CHD7||||||10.0030002593994|VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,]11:134014225]G|feature_truncation&coding_sequence_variant|HIGH|CHD7|55636|Transcript|NM_017780.4|protein_coding|30/38||||6499/11606|5982/8994|1994/2997||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||NA|||CHD7||||||10.0030002593994|VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus;MATEID=breakend2;MATE_BND_DEPTH=39;SVTYPE=BND;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr8	144085597	.	CAG	C	.	PASS	CSQ=-|frameshift_variant|HIGH|GPAA1|8733|Transcript|NM_003801.4|protein_coding|11/12||NM_003801.4:c.1477_1478del|NP_003792.1:p.Arg493GlyfsTer152|1574-1575/2054|1477-1478/1866|493/621|R/X|AGg/g|rs782339984|1||1||1|EntrezGene||||||||uncertain_significance&likely_pathogenic&pathogenic||1|||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.99191636|||||||AR||LP|7.56052e-05|0.99958|6.465e-05|6.056e-05|0||T|802447|criteria_provided&_conflicting_classifications|Conflicting_classifications_of_pathogenicity||||||||94.8258||0.992985||LP|filter&vkgl&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2:gt&gq&only_IP&vim&exit_u2
+chr9	104784352	.	AAAGAT	A	.	PASS	CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|50/50||NM_005502.4:c.6744_6748del|NP_005493.2:p.Phe2250ThrfsTer3|7057-7061/10408|6744-6748/6786|2248-2250/2261|TSF/TX|acATCTTtt/actt||1||-1||1|EntrezGene||||||||||||||||||||||||||||VUS|0.9937401|||||||AD&AR|||2.47816e-06|0.999862|5.8e-07|3.9e-07|0||T|||||||||||99.6014||0.985767||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2:gt&gq&only_IP&vim&exit_u2
+chr10	124402930	.	G	C	.	PASS	CSQ=C|stop_gained|HIGH|OAT|4942|Transcript|NM_000274.4|protein_coding|7/10||NM_000274.4:c.897C>G|NP_000265.1:p.Tyr299Ter|977/2039|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9577619|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001171814.2|protein_coding|6/9||NM_001171814.2:c.483C>G|NP_001165285.1:p.Tyr161Ter|749/1811|483/906|161/301|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9739149|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322965.2|protein_coding|7/10||NM_001322965.2:c.897C>G|NP_001309894.1:p.Tyr299Ter|972/2034|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9577619|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322966.2|protein_coding|8/11||NM_001322966.2:c.897C>G|NP_001309895.1:p.Tyr299Ter|1292/2354|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.91890144|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322967.2|protein_coding|8/11||NM_001322967.2:c.897C>G|NP_001309896.1:p.Tyr299Ter|1097/2159|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.95931506|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322968.2|protein_coding|9/12||NM_001322968.2:c.897C>G|NP_001309897.1:p.Tyr299Ter|1184/2246|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9648485|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322969.2|protein_coding|8/11||NM_001322969.2:c.897C>G|NP_001309898.1:p.Tyr299Ter|1064/2126|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9579952|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322970.2|protein_coding|9/12||NM_001322970.2:c.897C>G|NP_001309899.1:p.Tyr299Ter|1280/2342|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.91890144|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322971.2|protein_coding|5/8||NM_001322971.2:c.576C>G|NP_001309900.1:p.Tyr192Ter|656/1718|576/999|192/332|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96753824|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322974.2|protein_coding|7/10||NM_001322974.2:c.297C>G|NP_001309903.1:p.Tyr99Ter|863/1925|297/720|99/239|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&1&1|1&1&1|1737786&23076989&1609808&22674428||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.91896105|||||||AR||LP|4.83387e-05|0.99956|3.935e-05|3.64e-05|0||T|176|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.8435|0.96855|0.10738|1.28999996185303|LP|filter&vkgl&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	1|0:50:50:.:.:.:.	0|1:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:0:0:U2,U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr11	134144330	breakend2	G	G[8:61765143[	.	PASS	BND_DEPTH=39;CSQ=G[8:61765143[|feature_truncation&intron_variant|HIGH|JAM3|83700|Transcript|NM_001205329.2|protein_coding||3/7|||||||||1||1|||EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||NA|||JAM3||||||7.97399997711182|VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus,G[8:61765143[|feature_truncation&coding_sequence_variant|HIGH|JAM3|83700|Transcript|NM_032801.5|protein_coding|4/9||||359/3765|347/933|116/310||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||NA|||JAM3||||||7.97399997711182|VUS|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&str&annotSV&spliceAI&utr5&capice&exit_vus;MATEID=breakend1;MATE_BND_DEPTH=26;SVTYPE=BND;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr13	76995993	.	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_001366624.2|protein_coding|3/5||NM_001366624.2:c.431G>A|NP_001353553.1:p.Cys144Tyr|449/5286|431/594|144/197|C/Y|tGt/tAt|rs1566219136|1||1|||EntrezGene|||||0|0.99||pathogenic||1||||||||194|-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.9150198|||||||AR||LP||||||||623394|criteria_provided&_multiple_submitters&_no_conflicts|Pathogenic|||||||0.837|99.5193|0.99528|0.982568|10.0030002593994|LP|filter&vkgl&exit_lp,A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_006493.4|protein_coding|3/4||NM_006493.4:c.431G>A|NP_006484.2:p.Cys144Tyr|449/5243|431/1077|144/358|C/Y|tGt/tAt|rs1566219136|1||1||1|EntrezGene|||||0|0.998||pathogenic||1||||||||194|-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.98561203|||||||AR||LP||||||||623394|criteria_provided&_multiple_submitters&_no_conflicts|Pathogenic|||||||0.837|99.5193|0.99528|0.982568|10.0030002593994|LP|filter&vkgl&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr14	88870063	.	TG	T	.	PASS	CSQ=-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|12/16||NM_001288781.1:c.963del|NP_001275710.1:p.Met321IlefsTer15|1159/2378|963/1596|321/531|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic&pathogenic||1|19797195&21052717&16308660&30886724&16877420||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9973392|||||||AR||LP|7.43531e-06|0.99975|3.97e-06|3.13e-06|0||T|930561|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.7295||0.951635|9.52000045776367|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288782.1|protein_coding|10/14||NM_001288782.1:c.321del|NP_001275711.1:p.Met107IlefsTer15|1079/2298|321/954|107/317|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic&pathogenic||1|19797195&21052717&16308660&30886724&16877420||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9738995|||||||AR||LP|7.43531e-06|0.99975|3.97e-06|3.13e-06|0||T|930561|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.7295||0.951635|9.52000045776367|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding|11/15||NM_001288783.1:c.198del|NP_001275712.1:p.Met66IlefsTer15|1051/2270|198/831|66/276|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic&pathogenic||1|19797195&21052717&16308660&30886724&16877420||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9683613|||||||AR||LP|7.43531e-06|0.99975|3.97e-06|3.13e-06|0||T|930561|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.7295||0.951635|9.52000045776367|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|10/13||NM_001366535.2:c.885del|NP_001353464.1:p.Met295IlefsTer15|942/5160|885/1434|295/477|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic&pathogenic||1|19797195&21052717&16308660&30886724&16877420||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9943374|||||||AR||LP|7.43531e-06|0.99975|3.97e-06|3.13e-06|0||T|930561|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.7295||0.951635|9.52000045776367|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding|9/12||NM_001366536.2:c.795del|NP_001353465.1:p.Met265IlefsTer15|852/5070|795/1344|265/447|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic&pathogenic||1|19797195&21052717&16308660&30886724&16877420||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9970993|||||||AR||LP|7.43531e-06|0.99975|3.97e-06|3.13e-06|0||T|930561|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.7295||0.951635|9.52000045776367|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|11/15||NM_144596.4:c.915del|NP_653197.2:p.Met305IlefsTer15|972/2183|915/1548|305/515|M/X|atG/at|rs1431207606|1||1||1|EntrezGene||||||||likely_pathogenic&pathogenic||1|19797195&21052717&16308660&30886724&16877420||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9968413|||||||AR||LP|7.43531e-06|0.99975|3.97e-06|3.13e-06|0||T|930561|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.7295||0.951635|9.52000045776367|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|11/15||NM_198309.3:c.885del|NP_938051.1:p.Met295IlefsTer15|1081/2300|885/1518|295/505|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic&pathogenic||1|19797195&21052717&16308660&30886724&16877420||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98999304|||||||AR||LP|7.43531e-06|0.99975|3.97e-06|3.13e-06|0||T|930561|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.7295||0.951635|9.52000045776367|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding|10/14||NM_198310.3:c.795del|NP_938052.1:p.Met265IlefsTer15|991/2210|795/1428|265/475|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic&pathogenic||1|19797195&21052717&16308660&30886724&16877420||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.99751306|||||||AR||LP|7.43531e-06|0.99975|3.97e-06|3.13e-06|0||T|930561|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.7295||0.951635|9.52000045776367|LP|filter&vkgl&exit_lp,-|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|11/15||NR_159362.2:n.1002del||1002/5304|||||rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic&pathogenic||1|19797195&21052717&16308660&30886724&16877420||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.92329025|||||||AR||LP|7.43531e-06|0.99975|3.97e-06|3.13e-06|0||T|930561|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.7295||0.951635|9.52000045776367|LP|filter&vkgl&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|1:50:50:.:.:.:.	1|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2,U2,U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr14	104701523	.	T	G	.	PASS	CSQ=G|missense_variant|MODERATE|INF2|64423|Transcript|NM_001031714.4|protein_coding|2/22||NM_001031714.4:c.158T>G|NP_001026884.3:p.Leu53Arg|289/7566|158/3723|53/1240|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||102|-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9868581|||||||AD||LP|||||||||||||||||0.845|99.6723|0.94655|0.987499|7.84299993515015|LP|filter&vkgl&exit_lp,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_022489.4|protein_coding|2/23||NM_022489.4:c.158T>G|NP_071934.3:p.Leu53Arg|289/7623|158/3750|53/1249|L/R|cTg/cGg||1||1||1|EntrezGene|||||0|0.999||||||||||||102|-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.97871566|||||||AD||LP|||||||||||||||||0.845|99.6723|0.94655|0.987499|7.84299993515015|LP|filter&vkgl&exit_lp,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_032714.3|protein_coding|2/5||NM_032714.3:c.158T>G|NP_116103.1:p.Leu53Arg|289/1692|158/705|53/234|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||102|-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9679642|||||||AD||LP|||||||||||||||||0.845|99.6723|0.94655|0.987499|7.84299993515015|LP|filter&vkgl&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2,U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr17	31229046	.	AC	A	.	PASS	CSQ=-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|21/57||NM_000267.3:c.2433del|NP_000258.1:p.Ile812LeufsTer9|2816/12362|2433/8457|811/2818|T/X|acC/ac||1||1|||EntrezGene|||||||1||||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9995521|||||||AD||LP||||||||||||||||||99.8422||0.987342|3.78200006484985|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|21/58||NM_001042492.3:c.2433del|NP_001035957.1:p.Ile812LeufsTer9|2766/12373|2433/8520|811/2839|T/X|acC/ac||1||1||1|EntrezGene|||||||1||||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9997875|||||||AD||LP||||||||||||||||||99.8422||0.987342|3.78200006484985|LP|filter&vkgl&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:9:50:1:0:U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr17	31336861	.	T	G	.	PASS	CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|41/57||NM_000267.3:c.6311T>G|NP_000258.1:p.Leu2104Arg|6694/12362|6311/8457|2104/2818|L/R|cTg/cGg|rs1597843129&CM141499&CM143458|1||1|||EntrezGene|||||0|0.991||likely_pathogenic|0&1&1|1&1&1|24413922|||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.9602681|||||||AD||LP||||||||996527|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic|||||||0.861|99.6657|0.99296|0.98798|7.49399995803833|LP|filter&vkgl&exit_lp,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|42/58||NM_001042492.3:c.6374T>G|NP_001035957.1:p.Leu2125Arg|6707/12373|6374/8520|2125/2839|L/R|cTg/cGg|rs1597843129&CM141499&CM143458|1||1||1|EntrezGene|||||0|0.993||likely_pathogenic|0&1&1|1&1&1|24413922|||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.98705053|||||||AD||LP||||||||996527|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic|||||||0.861|99.6657|0.99296|0.98798|7.49399995803833|LP|filter&vkgl&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr19	11105470	.	C	G	.	PASS	CSQ=G|stop_gained|HIGH|LDLR|3949|Transcript|NM_000527.5|protein_coding|4/18||NM_000527.5:c.564C>G|NP_000518.1:p.Tyr188Ter|650/5173|564/2583|188/860|Y/*|taC/taG|rs121908034&CM920416&COSV99370340|1||1||1|EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&1&1|1&1&1|25741868&27765764&17142622&17539906&20809525&8882879&1734722&10422803&28645073&32041611||||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.99976677|||||||AD&AR||LP|1.85868e-06|0.999829|5e-07|1.4e-07|0||T|3727|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.9212|0.42365|0.549621|-0.108999997377396|LP|filter&vkgl&exit_lp,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195798.2|protein_coding|4/18||NM_001195798.2:c.564C>G|NP_001182727.1:p.Tyr188Ter|650/5167|564/2577|188/858|Y/*|taC/taG|rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&1&1|1&1&1|25741868&27765764&17142622&17539906&20809525&8882879&1734722&10422803&28645073&32041611||||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.9925931|||||||AD&AR||LP|1.85868e-06|0.999829|5e-07|1.4e-07|0||T|3727|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.9212|0.42365|0.549621|-0.108999997377396|LP|filter&vkgl&exit_lp,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195799.2|protein_coding|3/17||NM_001195799.2:c.441C>G|NP_001182728.1:p.Tyr147Ter|527/5050|441/2460|147/819|Y/*|taC/taG|rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&1&1|1&1&1|25741868&27765764&17142622&17539906&20809525&8882879&1734722&10422803&28645073&32041611||||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.986766|||||||AD&AR||LP|1.85868e-06|0.999829|5e-07|1.4e-07|0||T|3727|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.9212|0.42365|0.549621|-0.108999997377396|LP|filter&vkgl&exit_lp,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195800.2|protein_coding||3/15|NM_001195800.2:c.314-1922C>G|||||||rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&1&1|1&1&1|25741868&27765764&17142622&17539906&20809525&8882879&1734722&10422803&28645073&32041611||||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.0012291283|||||||AD&AR||LP|1.85868e-06|0.999829|5e-07|1.4e-07|0||T|3727|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.9212|0.42365|0.549621|-0.108999997377396|LP|filter&vkgl&exit_lp,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195803.2|protein_coding||3/15|NM_001195803.2:c.314-1095C>G|||||||rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&1&1|1&1&1|25741868&27765764&17142622&17539906&20809525&8882879&1734722&10422803&28645073&32041611||||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.0012291283|||||||AD&AR||LP|1.85868e-06|0.999829|5e-07|1.4e-07|0||T|3727|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.9212|0.42365|0.549621|-0.108999997377396|LP|filter&vkgl&exit_lp,G|downstream_gene_variant|MODIFIER|LDLR|3949|Transcript|NM_001406861.1|protein_coding||||||||||rs121908034&CM920416&COSV99370340|1|1990|1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&1&1|1&1&1|25741868&27765764&17142622&17539906&20809525&8882879&1734722&10422803&28645073&32041611||||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.0053919507|||||||AD&AR||LP|1.85868e-06|0.999829|5e-07|1.4e-07|0||T|3727|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.9212|0.42365|0.549621|-0.108999997377396|LP|filter&vkgl&exit_lp,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001219902|enhancer||||||||||rs121908034&CM920416&COSV99370340|1|||||||||||||pathogenic/likely_pathogenic&pathogenic|0&1&1|1&1&1|25741868&27765764&17142622&17539906&20809525&8882879&1734722&10422803&28645073&32041611|||||||||||||||||VUS|0.0024825744||||||||||1.85868e-06|0.999829|5e-07|1.4e-07|0||T|3727|criteria_provided&_multiple_submitters&_no_conflicts|Likely_pathogenic||||||||99.9212|0.42365|0.549621|-0.108999997377396|LP|filter&vkgl&clinVar&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	1/1:50:50:.:.:.:.	0|1:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	0|0:50:50:1:0:U2,U2,U2,U2,U2,U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chr19	17341188	.	GA	G	.	PASS	CSQ=-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001128855.3|protein_coding|8/9||NM_001128855.3:c.1058del|NP_001122327.1:p.Asn353ThrfsTer26|1117/2503|1058/1416|353/471|N/X|aAc/ac|rs2074427745|1||1|||EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.98709947|||||||AR||LP||||||||||||||||||99.0714||0.992573|5.86600017547607|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001195422.1|protein_coding|8/9||NM_001195422.1:c.1187del|NP_001182351.1:p.Asn396ThrfsTer26|1209/2595|1187/1545|396/514|N/X|aAc/ac|rs2074427745|1||1|||EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.9910253|||||||AR||LP||||||||||||||||||99.0714||0.992573|5.86600017547607|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_032620.4|protein_coding|8/9||NM_032620.4:c.1121del|NP_116009.2:p.Asn374ThrfsTer26|1180/2566|1121/1479|374/492|N/X|aAc/ac|rs2074427745|1||1||1|EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.99323684|||||||AR||LP||||||||||||||||||99.0714||0.992573|5.86600017547607|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_133644.4|protein_coding|7/8||NM_133644.4:c.1217del|NP_598399.2:p.Asn406ThrfsTer26|1276/2662|1217/1575|406/524|N/X|aAc/ac|rs2074427745|1||1|||EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.9919933|||||||AR||LP||||||||||||||||||99.0714||0.992573|5.86600017547607|LP|filter&vkgl&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	0|0:50:50:1:0:U2,U2,U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chrX	49075362	x_chrom	A	T	.	PASS	CSQ=T|splice_donor_variant|HIGH|WDR45|11152|Transcript|NM_001029896.2|protein_coding||9/10|NM_001029896.2:c.827+2T>A|||||||CS135341|1||-1||1|EntrezGene|||||||||1|1|||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9943469|||||||XL||LP||||||||||||||||||98.9917|0.96939|0.990133|8.11299991607666|LP|filter&vkgl&exit_lp,T|splice_donor_variant|HIGH|WDR45|11152|Transcript|NM_007075.4|protein_coding||10/11|NM_007075.4:c.830+2T>A|||||||CS135341|1||-1|||EntrezGene|||||||||1|1|||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9943469|||||||XL||LP||||||||||||||||||98.9917|0.96939|0.990133|8.11299991607666|LP|filter&vkgl&exit_lp,T|upstream_gene_variant|MODIFIER|PRAF2|11230|Transcript|NM_007213.3|protein_coding||||||||||CS135341|1|1360|-1|||EntrezGene|||||||||1|1|||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.973096|||||||||||||||||||||||||||98.9917|0.96939|0.990133|8.11299991607666|LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:50:50:.:.:.:.	0|0:10:50:.:.:.:.	1|0:50:50:1:0:U2,U2,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
+chrY	2787600	y_chrom	G	A	.	PASS	CSQ=A|stop_gained|HIGH|SRY|6736|Transcript|NM_003140.3|protein_coding|1/1||NM_003140.3:c.4C>T|NP_003131.1:p.Gln2Ter|83/828|4/615|2/204|Q/*|Caa/Taa|rs104894977&CM981858|1||-1||1|EntrezGene||||||||pathogenic|0&1|1&1|2401216&9443877||||||||-26|-50|2|-4|0.01|0.00|0.00|0.00|SRY|VUS|0.8103372|||||||YL||||||||||9753|no_assertion_criteria_provided|Pathogenic|||||||||0.79805|0.782253|-0.344999998807907|LP|filter&vkgl&clinVar&exit_lp;VIPC_S=U2	GT:DP:GQ:VID:VIM:VIPC_S:VIPP_S	1:50:50:.:.:.:.	.:.:50:.:.:.:.	1:50:50:.:.:.:.	.:.:50:.:.:.:.	0:10:50:.:.:.:.	1:50:50:1:0:U2:gt&gq&only_IP&vim&exit_u2

package/src/mocks/GRCh38/vcf/fixPaths.sql

@@ -0,0 +1,7 @@
+UPDATE appMetadata
+SET value = '{"uri":"placeholder.vcf","htsFormat":"VCF","genomeAssembly":"Unknown"}'
+WHERE id = 'htsFile';
+
+UPDATE appMetadata
+SET value = '-i placeholder.vcf -f -pb placeholder -pd placeholder.ped -m placeholder.json -tc placeholder.json -st placeholder.json -dt decisionTree.json -t placeholder.html -ph HP:placeholder'
+WHERE id = 'appArguments';

package/src/mocks/GRCh38/vcf/{no_vep.vcf.blob → no_vep.vcf}

@@ -208,7 +208,7 @@
 ##contig=<ID=chrEBV,length=171823>
 ##fileDate=20200320
 ##reference=file:/groups/umcg-gcc/tmp01/umcg-testdata/../vip/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Father	Mother	Nephew	Patient	Sister	Unrelated
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Father	MotherHasQuiteALongName	Nephew	Patient	Sister	Unrelated
 chr1	9982480	.	C	T	.	PASS	.	GT:DP:VIPC_S	0|0:10	0|0:50	0|0:50	1|0:50:U1	0|0:50	0|0:50
 chr1	16049917	n_alt	G	N	.	PASS	.	GT:DP:VIPC_S	1|0:11	0|0:50	0|0:50:U1	0|1:10	0|0:50	0|0:50
 chr1	17022720	star_alt	C	*	.	PASS	.	GT:DP:VIPC_S	0|0:50	0|0:50	0|0:50	1|0:50:U1	0|0:50	0|0:50