@molgenis/vip-report-template 8.1.0 → 8.2.1

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Files changed (10) hide show
  1. package/README.md +8 -7
  2. package/package.json +1 -1
  3. package/scripts/deploy_npm_registry.sh +1 -1
  4. package/src/components/GenomeBrowser.tsx +1 -1
  5. package/src/components/filter/typed/FilterCategorical.tsx +9 -2
  6. package/src/mocks/GRCh38/vcf/family.db.blob +0 -0
  7. package/src/mocks/GRCh38/vcf/family.vcf +31 -24
  8. package/src/mocks/config_vcf.json +2 -1
  9. package/src/utils/config/configFiltersComposed.ts +13 -1
  10. package/tests/utils/config/configFiltersComposed.test.ts +2 -0
package/README.md CHANGED
@@ -163,13 +163,14 @@ Filters can be given a default value using the "defaultValue" property.
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  The defaultValue is a string that should be properly formatted for the type of filters / values:
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- | filter / value type | format | examples |
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- |---------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------|
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- | string | any string. | "test" |
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- | interval (numbers) | comma separated string with a from and to value, if no comma is provided the value is used as the 'from' value. If only the 'to' value should be provided the string should start with a comma. | "1,100", ",100", "1" |
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- | locus | the format for this filter is: 'contig:form-to' or a string providing only the contig . | "chr1:1-10000000", "chrX" |
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- | categorical | comma separated string with the id's of the categories, '__null' is used for the 'unspecified' checkbox. | "LP,P", "cat1,cat2,__null" |
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- | flag / boolean | this is a special case of 'categorical' with categories 'true', 'false' and optionally '__null' | "true", "true,false,__null" |
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+ | filter / value type | format | examples |
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+ |---------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------|
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+ | string | any string. | "test" |
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+ | interval (numbers) | comma separated string with a from and to value, if no comma is provided the value is used as the 'from' value. If only the 'to' value should be provided the string should start with a comma. | "1,100", ",100", "1" |
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+ | locus | the format for this filter is: 'contig:form-to' or a string providing only the contig . | "chr1:1-10000000", "chrX" |
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+ | categorical* | comma separated string with the id's of the categories, '__null' is used for the 'unspecified' checkbox. Alternatively "non_null" can be provided as default value to indicate that all none null values should be selected. | "LP,P", "cat1,cat2,__null" |
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+ | flag / boolean | this is a special case of 'categorical' with categories 'true', 'false' and optionally '__null' | "true", "true,false,__null" |
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+
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  #### Sorts
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package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@molgenis/vip-report-template",
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- "version": "8.1.0",
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+ "version": "8.2.1",
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  "description": "Report Template for Variant Call Format (VCF) Report Generator",
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  "license": "LGPL-3.0",
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  "devDependencies": {
package/scripts/deploy_npm_registry.sh CHANGED
@@ -2,4 +2,4 @@
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  pnpm config set registry "https://registry.npmjs.org"
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  pnpm config set //registry.npmjs.org/:_authToken "${NPM_TOKEN}"
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  # workaround: packageManager is added to package.json after git checkout resulting in 'Unclean working tree' error
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- pnpm publish --no-git-checks .
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+ pnpm publish --no-git-checks .
package/src/components/GenomeBrowser.tsx CHANGED
@@ -85,7 +85,7 @@ const createBrowserConfig = async (
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  return {
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  reference: {
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- id: metadata.app.htsFile?.genomeAssembly,
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+ id: "Location:",
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  name: "Reference",
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  fastaURL: "data:application/gzip;base64," + fromByteArray(fastaGz),
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  },
package/src/components/filter/typed/FilterCategorical.tsx CHANGED
@@ -99,8 +99,15 @@ export const FilterCategorical: Component<FilterProps<ConfigFilterField, FilterV
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  onMount(() => {
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  if (props.config.defaultValue !== undefined && !props.isInited) {
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- const values = props.config.defaultValue.split(",");
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- validateValues(values, categories());
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+ let values;
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+ if (props.config.defaultValue === "non_null") {
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+ values = categories()
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+ .map((cat) => cat.id)
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+ .filter((id) => id !== "__null");
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+ } else {
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+ values = props.config.defaultValue.split(",");
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+ validateValues(values, categories());
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+ }
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  props.onValueChange({ value: values as FilterValueCategorical });
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  }
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  });
package/src/mocks/GRCh38/vcf/family.db.blob CHANGED
Binary file
package/src/mocks/GRCh38/vcf/family.vcf CHANGED
@@ -20,10 +20,12 @@
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  ##FORMAT=<ID=VIM,Number=1,Type=Integer,Description="Inheritance Match: Genotypes, affected statuses and known gene inheritance patterns match.">
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  ##FORMAT=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
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  ##FORMAT=<ID=VIPP_S,Number=.,Type=String,Description="VIP decision tree path.">
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+ ##GADO_PD=The GADO predicion for the relation between the phenotypes and the gene, HC: high confidence, LC: low confidence.
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+ ##GADO_SC=The combined prioritization GADO Z-score over the supplied HPO terms for this case.
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  ##Grantham=Grantham Matrix score - Grantham, R. Amino Acid Difference Formula to Help Explain Protein Evolution, Science 1974 Sep 6;185(4154):862-4.
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  ##HPO=List of HPO terms for the gene
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  ##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
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- ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|Grantham|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|existing_InFrame_oORFs|existing_OutOfFrame_oORFs|existing_uORFs|five_prime_UTR_variant_annotation|five_prime_UTR_variant_consequence|IncompletePenetrance|InheritanceModesGene|VKGL|VKGL_CL|gnomAD_AF|gnomAD_COV|gnomAD_FAF95|gnomAD_FAF99|gnomAD_HN|gnomAD_QC|gnomAD_SRC|clinVar_CLNID|clinVar_CLNREVSTAT|clinVar_CLNSIG|clinVar_CLNSIGINCL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|ASV_Gene_name|ASV_RE_gene|ALPHSCORE|ncER|FATHMM_MKL_NC|ReMM|phyloP|VIPC|VIPP">
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+ ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|Grantham|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|existing_InFrame_oORFs|existing_OutOfFrame_oORFs|existing_uORFs|five_prime_UTR_variant_annotation|five_prime_UTR_variant_consequence|HPO|GADO_PD|GADO_SC|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">
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  ##INFO=<ID=Disease,Number=1,Type=String,Description="Associated disorder">
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  ##INFO=<ID=DisplayRU,Number=1,Type=String,Description="Display repeat unit familiar to clinician">
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  ##INFO=<ID=HGNCId,Number=1,Type=Integer,Description="HGNC gene id for associated disease gene">
@@ -62,8 +64,8 @@
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  ##SpliceAI_pred_DS_DG=SpliceAI predicted effect on splicing. Delta score for donor gain
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  ##SpliceAI_pred_DS_DL=SpliceAI predicted effect on splicing. Delta score for donor loss
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  ##SpliceAI_pred_SYMBOL=SpliceAI gene symbol
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- ##VEP-command-line='vep --allele_number --allow_non_variant --assembly GRCh38 --buffer_size 1000 --cache --compress_output bgzip --custom [PATH]/hg38.phyloP100way.bw,phyloP,bigwig,exact,0 --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/plugins --dont_skip --exclude_predicted --fasta [PATH]/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --flag_pick_allele --fork 4 --format vcf --hgvs --input_file preprocessed_stranger_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'
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- ##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"
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+ ##VEP-command-line='vep --allele_number --allow_non_variant --assembly GRCh38 --buffer_size 1000 --cache --compress_output bgzip --custom [PATH]/hg38.phyloP100way.bw,phyloP,bigwig,exact,0 --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/plugins --dont_skip --exclude_predicted --fasta [PATH]/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --flag_pick_allele --fork 4 --format vcf --hgvs --input_file preprocessed_stranger_vip_normalized.vcf.gz --no_stats --numbers --offline --output_file vep_vip_annotated.vcf.gz --plugin [PATH]/hmtvar_trna_scores.tsv.gz --polyphen s --pubmed --refseq --safe --shift_3prime --sift s --symbol --total_length --use_given_ref --vcf'
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+ ##VEP="v111" time="2026-01-20 09:41:19" cache="/apps/data/vip/resources/vep/cache/homo_sapiens_refseq/111_GRCh38" ensembl-funcgen=111.5327cdd ensembl-variation=111.d616b1e ensembl=111.a6cc543 ensembl-io=111.dbba8d6 1000genomes="phase3" COSMIC="98" ClinVar="202306" HGMD-PUBLIC="20204" assembly="GRCh38.p14" dbSNP="156" gencode="GENCODE 45" genebuild="2014-07" gnomADe="r2.1.1" gnomADg="v3.1.2" polyphen="2.2.3" refseq="GCF_000001405.40-RS_2023_03 - GCF_000001405.40_GRCh38.p14_genomic.gff" regbuild="1.0" sift="6.2.1"
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  ##VIPC=VIP decision tree classification
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  ##VIPL=VIP decision tree labels (ampersand separated)
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  ##VIPP=VIP decision tree path (ampersand separated)
@@ -71,8 +73,10 @@
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  ##VIP_Version=4.0.1
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  ##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
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  ##VIP_treeVersion=2.2.0
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- ##VKGL=file:/apps/data/vip/resources/GRCh38/vkgl_consensus_20250401.tsv'
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+ ##VKGL=file:/apps/data/vip/resources/GRCh38/vkgl_consensus_20250701.tsv'
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  ##VKGL_CL=VKGL consensus variant classification.
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+ ##apogee_Score=Score assigned by APOGEE
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+ ##apogee_Uscore=Unbiased score assigned by APOGEE
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  ##clinVar_CLNID=ClinVar variation identifier
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  ##clinVar_CLNREVSTAT=ClinVar review status for the Variation ID
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  ##clinVar_CLNSIG=Clinical significance for this single variant; multiple values are separated by a vertical bar
@@ -285,28 +289,31 @@
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  ##gnomAD_HN=gnomAD number of homozygotes
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  ##gnomAD_QC=gnomAD quality control filters that failed
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  ##gnomAD_SRC=gnomAD source: E=exomes, G=genomes, T=total
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+ ##hmtvar_DiseaseScore=Disease score assigned by HmtVar
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+ ##mitoTip_Quartile=MitoTip Quartile
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+ ##mitoTip_Score=MitoTip Score
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  ##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.
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  ##reference=/vip/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
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  ##ALT=<ID=DEL,Description="Deletion">
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  ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance">
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- ##VIP_Version=8.4.5
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- ##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
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+ ##VIP_Version=9.0.0
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+ ##VIP_Command=/apps/data/vip/nextflow-24.10.6-dist -C /apps/software/vip/v9.0.0/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/v9.0.0/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/
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  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Unrelated Sister Nephew MotherHasQuiteALongName Father Patient
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- 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
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- 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
297
- 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
298
- 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
299
- 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
300
- 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
301
- 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
302
- 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
303
- 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
304
- 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
305
- 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,U1,U2,U2,U2,U2,U2,U1,U2:gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u1,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_u1,gt&gq&only_IP&vim&exit_u2,gt&gq&only_IP&vim&exit_u2
306
- 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
307
- 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
308
- 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
309
- 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
310
- 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
311
- 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
312
- 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
302
+ 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||||||HP:0000505&HP:0001250||-0.821||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||||||HP:0000505&HP:0001250||-0.821||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||||||HP:0000505&HP:0001250||-0.821||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|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
303
+ 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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||0.536||AD&AR||||||||||||||NA|||MSH2||||||||||||VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&gnomAD&gnomAD_AF&sv&str&annotSV&spl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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
304
+ 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||||||HP:0001250||1.575||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||||||HP:0001250||1.575||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||||||HP:0001250||1.575||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||||||HP:0001250||1.575||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
305
+ 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||||||HP:0001250||-0.145||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
306
+ 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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||1.125||AD||||||||||||||NA|||CHD7|||||||||||10.0030002593994|VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0000505&HP:0001250||1.125||AD||||||||||||||NA|||CHD7|||||||||||10.0030002593994|VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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
307
+ 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||||||HP:0000505&HP:0001250||2.946||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
308
+ 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||||||HP:0000505||-0.691||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&is_mtdna&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
309
+ 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||||||HP:0000505&HP:0001250||-0.504||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||||||HP:0000505&HP:0001250||-0.504||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||||||HP:0000505&HP:0001250||-0.504||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||||||HP:0000505&HP:0001250||-0.504||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||||||HP:0000505&HP:0001250||-0.504||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||||||HP:0000505&HP:0001250||-0.504||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||||||HP:0000505&HP:0001250||-0.504||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||||||HP:0000505&HP:0001250||-0.504||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||||||HP:0000505&HP:0001250||-0.504||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||||||HP:0000505&HP:0001250||-0.504||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
310
+ 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|||||||||||||||||||||||||||||||||||HP:0001250||0.199||AR||||||||||||||NA|||JAM3|||||||||||7.97399997711182|VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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|||||||||||||||||||||||||||||||||||HP:0001250||0.199||AR||||||||||||||NA|||JAM3|||||||||||7.97399997711182|VUS|filter&vkgl&clinVar&chrom&gene&is_mtdna&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
311
+ 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||||||HP:0000505&HP:0001250||-1.414||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||||||HP:0000505&HP:0001250||-1.414||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
312
+ 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||||||HP:0000505&HP:0000556&HP:0001250||1.217||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||||||HP:0000505&HP:0000556&HP:0001250||1.217||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||||||HP:0000505&HP:0000556&HP:0001250||1.217||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||||||HP:0000505&HP:0000556&HP:0001250||1.217||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||||||HP:0000505&HP:0000556&HP:0001250||1.217||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||||||HP:0000505&HP:0000556&HP:0001250||1.217||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||||||HP:0000505&HP:0000556&HP:0001250||1.217||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||||||HP:0000505&HP:0000556&HP:0001250||1.217||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||||||HP:0000505&HP:0000556&HP:0001250||1.217||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
313
+ 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||||||||-0.357||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||||||||-0.357||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||||||||-0.357||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
314
+ 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||||||HP:0000505&HP:0001250||1.215||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||||||HP:0000505&HP:0001250||1.215||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
315
+ 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||||||HP:0000505&HP:0001250||1.215||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||||||HP:0000505&HP:0001250||1.215||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
316
+ 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||||||||-0.617||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||||||||-0.617||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||||||||-0.617||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||||||||-0.617||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||||||||-0.617||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||||||||-0.617||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:.:.:.:. 1|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
317
+ 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||||||HP:0000505&HP:0001250||0.729||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||||||HP:0000505&HP:0001250||0.729||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||||||HP:0000505&HP:0001250||0.729||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||||||HP:0000505&HP:0001250||0.729||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:.:.:.:. 1|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
318
+ 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||||||HP:0000505&HP:0001250||-0.785||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||||||HP:0000505&HP:0001250||-0.785||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||||||||1.419||||||||||||||||||||||98.9917|0.96939|0.990133||||||8.11299991607666|LP|filter&vkgl&clinVar&chrom&gene&is_mtdna&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
319
+ 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||||||HP:0000505||||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/config_vcf.json CHANGED
@@ -481,7 +481,8 @@
481
481
  {
482
482
  "type": "composed",
483
483
  "name": "hpo",
484
- "label": "Gene-phenotype association (HPO)"
484
+ "label": "Gene-phenotype association (HPO)",
485
+ "defaultValue": "non_null"
485
486
  },
486
487
  {
487
488
  "type": "info",
package/src/utils/config/configFiltersComposed.ts CHANGED
@@ -13,6 +13,7 @@ import { ConfigJsonFilterComposed, ConfigVip } from "../../types/config";
13
13
  import { getDescription, getLabel } from "./config.ts";
14
14
  import { getInfoNestedField, getSampleField, getSampleFields, parseContigIds } from "../vcf.ts";
15
15
  import { ConfigInvalidError } from "../error.ts";
16
+ import { CategoryRecord } from "@molgenis/vip-report-vcf";
16
17
 
17
18
  export function initConfigFilterComposed(
18
19
  config: ConfigJsonFilterComposed,
@@ -60,13 +61,24 @@ function createConfigFilterHpo(
60
61
  const fieldCsqHpo = getInfoNestedField(metadata, "CSQ", "HPO");
61
62
  if (fieldCsqHpo === undefined) return null;
62
63
 
64
+ const csqCategories: CategoryRecord | undefined = fieldCsqHpo.categories;
65
+
63
66
  const filterField = {
64
67
  // create field with categories based on the sample hpo terms
65
68
  ...fieldCsqHpo,
66
69
  categories: sample.phenotypes.reduce(
67
70
  (acc, phenotype) => ({
68
71
  ...acc,
69
- [phenotype.type.id]: { label: phenotype.type.label },
72
+ [phenotype.type.id]: {
73
+ label:
74
+ csqCategories !== undefined && csqCategories[phenotype.type.id] !== undefined
75
+ ? csqCategories[phenotype.type.id]!.label
76
+ : phenotype.type.label,
77
+ description:
78
+ csqCategories !== undefined && csqCategories[phenotype.type.id] !== undefined
79
+ ? csqCategories[phenotype.type.id]!.description
80
+ : phenotype.type.label,
81
+ },
70
82
  }),
71
83
  {},
72
84
  ),
package/tests/utils/config/configFiltersComposed.test.ts CHANGED
@@ -62,9 +62,11 @@ describe("config filters composed", () => {
62
62
  ...fieldHpo,
63
63
  categories: {
64
64
  "HP:0000951": {
65
+ description: "HP:0000951 label",
65
66
  label: "HP:0000951 label",
66
67
  },
67
68
  "HP:0000952": {
69
+ description: "HP:0000952 label",
68
70
  label: "HP:0000952 label",
69
71
  },
70
72
  },