@molgenis/vip-report-template 7.1.2 → 8.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.gitattributes +3 -1
- package/.travis.yml +1 -0
- package/README.md +13 -0
- package/eslint.config.mjs +6 -1
- package/package.json +6 -5
- package/scripts/validateConfig/README.txt +5 -0
- package/scripts/validateConfig/compileValidator.ts +17 -0
- package/scripts/validateConfig/createSchema.ts +6 -0
- package/scripts/validateConfig/schema.ts +370 -0
- package/src/App.tsx +2 -1
- package/src/components/DatasetDropdown.tsx +1 -1
- package/src/components/GenomeBrowser.tsx +14 -4
- package/src/components/RecordsTable.tsx +23 -6
- package/src/components/VariantConsequenceContainer.tsx +9 -2
- package/src/components/VariantInfoTable.tsx +1 -1
- package/src/components/VariantsContainer.tsx +47 -9
- package/src/components/VariantsContainerHeader.tsx +1 -8
- package/src/components/field/composed/FieldGenotype.tsx +1 -1
- package/src/components/field/composed/FieldGenotypeStr.tsx +18 -10
- package/src/components/field/composed/FieldGnomAd.tsx +1 -1
- package/src/components/field/composed/FieldInheritanceModes.tsx +1 -4
- package/src/components/field/composed/FieldVkgl.tsx +1 -1
- package/src/components/field/typed/FieldCategorical.tsx +1 -1
- package/src/components/field/typed/FieldCharacter.tsx +1 -1
- package/src/components/field/typed/FieldFlag.tsx +1 -1
- package/src/components/field/typed/FieldFloat.tsx +1 -1
- package/src/components/field/typed/FieldInteger.tsx +1 -1
- package/src/components/field/typed/FieldString.tsx +1 -1
- package/src/components/filter/Filter.tsx +1 -0
- package/src/components/filter/composed/FilterAllelicImbalance.tsx +1 -0
- package/src/components/filter/composed/FilterComposed.tsx +7 -0
- package/src/components/filter/composed/FilterDeNovo.tsx +1 -0
- package/src/components/filter/composed/FilterHpo.tsx +1 -0
- package/src/components/filter/composed/FilterInheritance.tsx +1 -0
- package/src/components/filter/composed/FilterLocus.tsx +17 -3
- package/src/components/filter/composed/FilterPick.tsx +30 -0
- package/src/components/filter/composed/FilterVipC.tsx +1 -0
- package/src/components/filter/composed/FilterVipCS.tsx +1 -0
- package/src/components/filter/fixed/FilterFixed.tsx +7 -0
- package/src/components/filter/typed/FilterCategorical.tsx +18 -1
- package/src/components/filter/typed/FilterFlag.tsx +2 -0
- package/src/components/filter/typed/FilterInterval.tsx +29 -1
- package/src/components/filter/typed/FilterString.tsx +8 -1
- package/src/components/filter/typed/FilterTyped.tsx +1 -0
- package/src/components/form/ButtonApply.tsx +6 -2
- package/src/mocks/GRCh38/README.txt +15 -0
- package/src/mocks/GRCh38/decisionTree.json +201 -0
- package/src/mocks/GRCh38/family.ped +6 -0
- package/src/mocks/GRCh38/field_metadata.json +36 -11
- package/src/mocks/GRCh38/sample1.ped +1 -0
- package/src/mocks/GRCh38/static.ts +36 -148
- package/src/mocks/GRCh38/str.ped +1 -0
- package/src/mocks/GRCh38/vcf/family.db.blob +0 -0
- package/src/mocks/GRCh38/vcf/family.vcf +312 -0
- package/src/mocks/GRCh38/vcf/fixPaths.sql +7 -0
- package/src/mocks/GRCh38/vcf/no_vep.db.blob +0 -0
- package/src/mocks/GRCh38/vcf/{no_vep.vcf.blob → no_vep.vcf} +1 -1
- package/src/mocks/GRCh38/vcf/samples_0.db.blob +0 -0
- package/src/mocks/GRCh38/vcf/samples_1.db.blob +0 -0
- package/src/mocks/GRCh38/vcf/samples_100.db.blob +0 -0
- package/src/mocks/GRCh38/vcf/{samples_100.vcf.blob → samples_100.vcf} +6 -6
- package/src/mocks/GRCh38/vcf/str.db.blob +0 -0
- package/src/mocks/GRCh38/vcf/{str.vcf.blob → str.vcf} +17 -17
- package/src/mocks/MockApiClient.ts +60 -226
- package/src/mocks/config_cram.json +4 -0
- package/src/mocks/config_default_values.json +722 -0
- package/src/mocks/config_vcf.json +15 -1
- package/src/mocks/sql-wasm.wasm.blob +0 -0
- package/src/types/config.d.ts +9 -5
- package/src/types/configCells.d.ts +1 -0
- package/src/types/configFilter.d.ts +1 -0
- package/src/types/configFilterComposed.d.ts +3 -0
- package/src/utils/api.ts +21 -49
- package/src/utils/config/configCellsComposed.ts +1 -1
- package/src/utils/config/configCellsField.ts +2 -0
- package/src/utils/config/configFiltersComposed.ts +7 -0
- package/src/utils/config/configFiltersField.ts +3 -2
- package/src/utils/config/configFiltersFixed.ts +7 -0
- package/src/utils/config/configValidator.precompiled.ts +83402 -0
- package/src/utils/config/configValidator.ts +3 -368
- package/src/utils/csq.ts +5 -10
- package/src/utils/decisionTree.ts +8 -9
- package/src/utils/query/query.ts +3 -2
- package/src/utils/query/queryFilter.ts +2 -3
- package/src/utils/query/queryFilterComposed.ts +12 -12
- package/src/utils/query/queryFilterField.ts +14 -7
- package/src/utils/query/queryFilterFixed.ts +5 -5
- package/src/utils/query/querySample.ts +15 -4
- package/src/utils/query/selector.ts +5 -20
- package/src/utils/query/sort.ts +4 -4
- package/src/utils/vcf.ts +20 -11
- package/src/views/Help.tsx +2 -2
- package/src/views/SampleVariant.tsx +4 -1
- package/src/views/Samples.tsx +10 -3
- package/src/views/data/data.tsx +2 -2
- package/tests/utils/config/configFiltersComposed.test.ts +2 -0
- package/tests/utils/config/configFiltersField.test.ts +4 -2
- package/tests/utils/config/configFiltersFixed.test.ts +23 -6
- package/tests/utils/query/query.test.ts +34 -6
- package/tests/utils/query/queryFilter.test.ts +4 -31
- package/tests/utils/query/queryFilterComposed.test.ts +13 -13
- package/tests/utils/query/queryFilterField.test.ts +5 -5
- package/tests/utils/query/queryFilterFixed.test.ts +5 -5
- package/tests/utils/query/querySample.test.ts +50 -10
- package/tests/utils/query/sort.test.ts +1 -1
- package/tests/utils/vcf.test.ts +1 -0
- package/vite.config.mts +2 -1
- package/src/mocks/GRCh37/alignment.cram.blob +0 -0
- package/src/mocks/GRCh37/alignment.cram.crai.blob +0 -0
- package/src/mocks/GRCh37/decisionTree.json +0 -355
- package/src/mocks/GRCh37/fasta/1-10042288-10042788.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-152520538-152521038.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-16375333-16375833.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-16376162-16376662.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-17348965-17349469.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-17348969-17349469.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/1-17354844-17355344.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/10-126091249-126091749.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/11-134013975-134014475.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/13-77569878-77570378.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/14-105167610-105168110.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/14-89307588-89308088.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/14-89309945-89310445.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/14-89336157-89336657.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29555814-29556314.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29585172-29585672.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29663629-29664129.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29675976-29676476.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/17-29683733-29684233.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/19-11215896-11216396.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/19-11223801-11224301.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/19-17449149-17449649.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/19-17451747-17452247.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/2-47635417-47635917.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/20-62326742-62327242.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/22-50627343-50627843.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/22-50721296-50721796.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/4-106320044-106320544.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/7-42017061-42017561.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/7-42064707-42065207.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/8-145140250-145140750.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/8-61764893-61765393.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/9-107546383-107546883.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/9-107584614-107585114.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/MT-15076-15576.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/X-48932771-48933271.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/fasta/Y-2655391-2655891.fasta.gz.blob +0 -0
- package/src/mocks/GRCh37/field_metadata.json +0 -794
- package/src/mocks/GRCh37/genes.gff.gz.blob +0 -0
- package/src/mocks/GRCh37/sampleTree.json +0 -143
- package/src/mocks/GRCh37/static.ts +0 -189
- package/src/mocks/GRCh37/vcf/family.vcf.blob +0 -134
- package/src/mocks/GRCh38/vcf/family.vcf.blob +0 -272
- package/src/mocks/static.ts +0 -1636
- /package/src/mocks/GRCh38/vcf/{samples_0.vcf.blob → samples_0.vcf} +0 -0
- /package/src/mocks/GRCh38/vcf/{samples_1.vcf.blob → samples_1.vcf} +0 -0
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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##ALT=<ID=DEL,Description="Deletion">
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##ASV_ACMG_class=AnnotSv 'ACMG_class' output.
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##ASV_AnnotSV_ranking_criteria=AnnotSv 'AnnotSV_ranking_criteria' output.
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##ASV_AnnotSV_ranking_score=AnnotSv 'AnnotSV_ranking_score' output.
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##CAPICE_CL=CAPICE classification
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##CAPICE_SC=CAPICE score
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##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
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##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FORMAT=<ID=VI,Number=.,Type=String,Description="An enumeration of possible inheritance modes.">
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##FORMAT=<ID=VIC,Number=1,Type=String,Description="Possible Compound hetrozygote variants.">
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##FORMAT=<ID=VID,Number=1,Type=Integer,Description="Inheritance Denovo status.">
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##FORMAT=<ID=VIG,Number=.,Type=String,Description="Genes with an inheritance match.">
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##FORMAT=<ID=VIM,Number=1,Type=Integer,Description="Inheritance Match status.">
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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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##FORMAT=<ID=VIS,Number=.,Type=String,Description="An enumeration of possible sub inheritance modes like e.g. compound, non penetrance.">
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##GADO_PD=The GADO prediction 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|HPO|GADO_PD|GADO_SC|IncompletePenetrance|InheritanceModesGene|VKGL|VKGL_CL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|phyloP|gnomAD|gnomAD_AF|gnomAD_HN|clinVar|clinVar_CLNSIG|clinVar_CLNSIGINCL|clinVar_CLNREVSTAT|VIPC|VIPP">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
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##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
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##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
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##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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##INFO=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification (samples).">
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##INFO=<ID=clinVar,Number=.,Type=String,Description="/groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/clinvar_20220620.vcf.gz (exact)">
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##INFO=<ID=clinVar_CLNREVSTAT,Number=.,Type=String,Description="CLNREVSTAT field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/clinvar_20220620.vcf.gz">
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##INFO=<ID=clinVar_CLNSIG,Number=.,Type=String,Description="CLNSIG field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/clinvar_20220620.vcf.gz">
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##INFO=<ID=clinVar_CLNSIGINCL,Number=.,Type=String,Description="CLNSIGINCL field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/clinvar_20220620.vcf.gz">
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##INFO=<ID=gnomAD,Number=.,Type=String,Description="/groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz (exact)">
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##INFO=<ID=gnomAD_AF,Number=.,Type=String,Description="AF field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
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##INFO=<ID=gnomAD_HN,Number=.,Type=String,Description="HN field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
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##INFO=<ID=phyloP,Number=.,Type=String,Description="/groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/resources/GRCh37/hg19.100way.phyloP100way.bed.gz">
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##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance.
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##InheritanceModesGene=List of inheritance modes for the gene
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##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
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##SpliceAI_pred_DP_AL=SpliceAI predicted effect on splicing. Delta position for acceptor loss
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##SpliceAI_pred_DP_DG=SpliceAI predicted effect on splicing. Delta position for donor gain
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##SpliceAI_pred_DP_DL=SpliceAI predicted effect on splicing. Delta position for donor loss
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##SpliceAI_pred_DS_AG=SpliceAI predicted effect on splicing. Delta score for acceptor gain
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##SpliceAI_pred_DS_AL=SpliceAI predicted effect on splicing. Delta score for acceptor loss
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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 GRCh37 --buffer_size 1000 --cache --compress_output bgzip --custom [PATH]/clinvar_20230604.vcf.gz,clinVar,vcf,exact,0,CLNSIG,CLNSIGINCL,CLNREVSTAT --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/plugins --dont_skip --exclude_predicted --fasta [PATH]/human_g1k_v37.fasta.gz --flag_pick_allele --fork 4 --format vcf --hgvs --input_file vip_normalized.vcf.gz --no_stats --numbers --offline --output_file vip_annotated.vcf.gz --plugin [PATH]/vkgl_consensus_20230401.tsv,1 --plugin AnnotSV,vip_normalized.vcf.gz.tsv,AnnotSV_ranking_score;AnnotSV_ranking_criteria;ACMG_class --polyphen s --pubmed --refseq --safe --shift_3prime --sift s --symbol --total_length --use_given_ref --vcf'
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##VEP="v109" time="2023-07-06 06:31:06" cache="/groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/resources/vep/cache/homo_sapiens_refseq/109_GRCh37" ensembl-funcgen=109.cba2db8 ensembl-variation=109.18a12b6 ensembl=109.10baaec ensembl-io=109.4946a86 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomADe="r2.1" polyphen="2.2.2" refseq="2020-10-26 17:03:42 - GCF_000001405.25_GRCh37.p13_genomic.gff" regbuild="1.0" sift="sift5.2.2"
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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)
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##VIP_Command=nextflow run ./main.nf --input /groups/solve-rd/tmp10/bcharbon/testdata/testdata_b37.vcf --output /groups/solve-rd/tmp10/projects/vip/testdata_out --keep --pedigree /groups/solve-rd/tmp10/bcharbon/example.ped --probands Patient --phenotypes 'HP:0000951;HP:0003124' --assembly GRCh37 --param_with_equals_sign x=y
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##VIP_Version=4.3.0
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##VIP_treeCommand=--input testdata_b37_chunk0_annotated.vcf.gz --config /groups/solve-rd/tmp10/projects/vip/git/vip/resources/decision_tree.json --labels 0 --path 0 --output testdata_b37_chunk0_classified.vcf.gz
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##VIP_treeVersion=3.0.0
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##VKGL=file:/groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/resources/GRCh37/vkgl_consensus_20230401.tsv'
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##VKGL_CL=VKGL consensus variant classification.
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##contig=<ID=1,length=249250621,assembly=b37>
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##contig=<ID=2,length=243199373,assembly=b37>
|
|
66
|
-
##contig=<ID=3,length=198022430,assembly=b37>
|
|
67
|
-
##contig=<ID=4,length=191154276,assembly=b37>
|
|
68
|
-
##contig=<ID=5,length=180915260,assembly=b37>
|
|
69
|
-
##contig=<ID=6,length=171115067,assembly=b37>
|
|
70
|
-
##contig=<ID=7,length=159138663,assembly=b37>
|
|
71
|
-
##contig=<ID=8,length=146364022,assembly=b37>
|
|
72
|
-
##contig=<ID=9,length=141213431,assembly=b37>
|
|
73
|
-
##contig=<ID=10,length=135534747,assembly=b37>
|
|
74
|
-
##contig=<ID=11,length=135006516,assembly=b37>
|
|
75
|
-
##contig=<ID=12,length=133851895,assembly=b37>
|
|
76
|
-
##contig=<ID=13,length=115169878,assembly=b37>
|
|
77
|
-
##contig=<ID=14,length=107349540,assembly=b37>
|
|
78
|
-
##contig=<ID=15,length=102531392,assembly=b37>
|
|
79
|
-
##contig=<ID=16,length=90354753,assembly=b37>
|
|
80
|
-
##contig=<ID=17,length=81195210,assembly=b37>
|
|
81
|
-
##contig=<ID=18,length=78077248,assembly=b37>
|
|
82
|
-
##contig=<ID=19,length=59128983,assembly=b37>
|
|
83
|
-
##contig=<ID=20,length=63025520,assembly=b37>
|
|
84
|
-
##contig=<ID=21,length=48129895,assembly=b37>
|
|
85
|
-
##contig=<ID=22,length=51304566,assembly=b37>
|
|
86
|
-
##contig=<ID=X,length=155270560,assembly=b37>
|
|
87
|
-
##contig=<ID=Y,length=59373566,assembly=b37>
|
|
88
|
-
##contig=<ID=MT,length=16569,assembly=b37>
|
|
89
|
-
##existing_InFrame_oORFs=The number of existing inFrame overlapping ORFs (inFrame oORF) at the 5 prime UTR
|
|
90
|
-
##existing_OutOfFrame_oORFs=The number of existing out-of-frame overlapping ORFs (OutOfFrame oORF) at the 5 prime UTR
|
|
91
|
-
##existing_uORFs=The number of existing uORFs with a stop codon within the 5 prime UTR
|
|
92
|
-
##fileDate=20200320
|
|
93
|
-
##five_prime_UTR_variant_annotation=Output the annotation of a given 5 prime UTR variant
|
|
94
|
-
##five_prime_UTR_variant_consequence=Output the variant consequences of a given 5 prime UTR variant: uAUG_gained, uAUG_lost, uSTOP_lost or uFrameshift
|
|
95
|
-
##VIP_Version=5.6.0
|
|
96
|
-
##VIP_Command=nextflow -C /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/config/nxf_vcf.config,/groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio/custom.cfg -log /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio/.nxf.log run /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/vip_vcf.nf -offline -profile slurm -with-report /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio/nxf_report.html -with-timeline /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio/nxf_timeline.html --input /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/resources/snv_proband_trio.tsv --output /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio -resume
|
|
97
|
-
##INFO=<ID=DisplayRU,Number=1,Type=String,Description="Display repeat unit familiar to clinician">
|
|
98
|
-
##FORMAT=<ID=REPCI,Number=1,Type=String,Description="Confidence interval for REPCN">
|
|
99
|
-
##FORMAT=<ID=REPCN,Number=1,Type=String,Description="Number of repeat units spanned by the allele">
|
|
100
|
-
##INFO=<ID=STR_NORMAL_MAX,Number=1,Type=Integer,Description="Max number of repeats allowed to call as normal">
|
|
101
|
-
##INFO=<ID=STR_PATHOLOGIC_MIN,Number=1,Type=Integer,Description="Min number of repeats required to call as pathologic">
|
|
102
|
-
##INFO=<ID=STR_STATUS,Number=A,Type=String,Description="Repeat expansion status. Alternatives in [normal, pre_mutation, full_mutation]">
|
|
103
|
-
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient Father MotherHasQuiteALongName Sister Nephew Unrelated
|
|
104
|
-
1 1701 . T C . PASS CSQ=C|intergenic_variant|MODIFIER||||||||||||||||1||||1||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|exit_rm;DP=131;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:64802:.:OK:GQ&DP&VIM&VID&exit_u1 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
|
|
105
|
-
1 10042538 . 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||1|EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||101|0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.13080463||||||||1.09||AR||LP||||3.917000|1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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||1&1|26103963&22842229&22842230||||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.12802194||||||||1.09||AR||LP||||3.917000|1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||101|0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.14871566||||||||1.09||AR||LP||||3.917000|1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=LQ GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:10:AR:1:64802:1:U3,U3,U3:GQ&exit_u3,GQ&exit_u3,GQ&exit_u3 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
|
|
106
|
-
1 16375583 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1|||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032756623||||||HP:0000951||1.439||AR||LP||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,-|frameshift_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding|1/13||NM_001165945.2:c.118del|NP_001159417.2:p.Arg40GlyfsTer4|328/2174|118/1554|40/517|R/X|Agg/gg|rs751608665|1||1|||EntrezGene||||||||uncertain_significance&pathogenic||1|||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.9124473||||||HP:0000951||1.439||AR||LP||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000001994|promoter||||||||||rs751608665|1|||||||||||||uncertain_significance&pathogenic||1|||||||||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000922299|CTCF_binding_site||||||||||rs751608665|1|||||||||||||uncertain_significance&pathogenic||1|||||||||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00533524886|||||||||||rs751608665|1||1|||||||||||uncertain_significance&pathogenic||1|||ENSPFM0617|1|N||ZBTB7B&ZBTB7A&ZBTB7C||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00529659450|||||||||||rs751608665|1||1|||||||||||uncertain_significance&pathogenic||1|||ENSPFM0566|3|N||TEAD4::MAX||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00529435523|||||||||||rs751608665|1||1|||||||||||uncertain_significance&pathogenic||1|||ENSPFM0544|3|N||TEAD4::FIGLA||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00910553844|||||||||||rs751608665|1||1|||||||||||uncertain_significance&pathogenic||1|||ENSPFM0383|17|N||MGA::EVX1||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S:VIS 1|0:25,25:50:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1:AR_C 1|0:25,25:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:.
|
|
107
|
-
1 16376412 n_alt G N . PASS CSQ=N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19||||||||CS1211892&CS971662|1||1||1|EntrezGene||||||||||1&1||||||||||||||||||VUS|0.9316635||||||HP:0000951||1.439||AR||||||4.909000||||||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12||||||||CS1211892&CS971662|1||1|||EntrezGene||||||||||1&1||||||||||||||||||VUS|0.9316635||||||HP:0000951||1.439||AR||||||4.909000||||||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S:VIS 1|0:5,45:50:.:AR_C,AD:1_16376412_G_A,1_16375583_GA_G:1:1188:1:OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:.
|
|
108
|
-
1 16376412 . G A . PASS CSQ=A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19|NM_000085.5:c.968+1G>A|||||||rs201204502&CS1211892&CS971662|1||1||1|EntrezGene||||||||||0&1&1|||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9882061||||||HP:0000951||1.439||AR||LP||||4.909000|1:16376412-16376412|6.38086e-05|0|1285112|Likely_pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12|NM_001165945.2:c.461+1G>A|||||||rs201204502&CS1211892&CS971662|1||1|||EntrezGene||||||||||0&1&1|||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9882061||||||HP:0000951||1.439||AR||LP||||4.909000|1:16376412-16376412|6.38086e-05|0|1285112|Likely_pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S:VIS 0|1:50:50:50:AR:1_16375583_GA_G,1_16376412_G_N:0:1188:1:OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:.
|
|
109
|
-
1 17349219 g_ref G A . PASS CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||0|1||likely_pathogenic|0&0&0&1|1&1&1&1||||||||180|28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.9769107||||||HP:0000951||2.452||AD&AR||LP||||9.093000||||183735|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:19:19:AR:1:6390:1:OK:GQ&DP&VIM&exit_u1 1|0:45,5:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
|
|
110
|
-
1 17355094 . C T . PASS CSQ=T|splice_donor_variant|HIGH|SDHB|6390|Transcript|NM_003000.3|protein_coding||4/7|NM_003000.3:c.423+1G>A|||||||rs398122805&CS056774&CS062098&COSV64965540|1||-1||1|EntrezGene||||||||pathogenic|0&0&0&1|1&1&1&1|21348866&17667967&17804857&16405730&21565294&15383933||||||||-49|12|26|1|0.00|0.00|0.14|0.97|SDHB|VUS|0.991252||||||HP:0000951||2.452||AD&AR||LP||||7.131000|1:17355094-17355094|1.19344e-05|0|29896|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:5,45:50:50:AD:1:6390:1:OK:GQ&DP&VIM&exit_u1 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
|
|
111
|
-
1 152520788 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|upstream_gene_variant|MODIFIER|LCE3C|353144|Transcript|NM_178434.3|protein_coding|||||||||||1|2608|1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946440||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787329||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013752||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946442||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946443||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001505919||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787330||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787331||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787332||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00701519957||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00905971885||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00522719201||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm;SVLEN=-49314;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S:VIC 1|1:0,50:50:50:AR:1:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1:123456_A_C 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.
|
|
112
|
-
2 321682 . T <DEL> . PASS CSQ=deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|LINC01865|105373350|Transcript|NR_146953.1|lncRNA|3/4|3/3|||685-?/2100||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||||||||3|1A_(cf_Gene_count%2C_RE_gene%2C_+0.00)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(1_gene%2C_+0.00)%3B5F_(+0.00)|0.0|||||||||VUS|filter&vkgl&clinVar&gnomAD&sv&annotSV&exit_vus;END=321887;SVLEN=-205;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:0:64802:.:OK:GQ&DP&VIM&VID&exit_u1 1|0:50,0:50:50:.:.:.:.:.:. 1|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
|
|
113
|
-
2 6693415 . T <DEL> . PASS CSQ=deletion|regulatory_region_ablation®ulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001914803||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524064657||||||||||||1||||1|||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524052275||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524121752||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524688093||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00525576244||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524108762||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524259723||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524175972||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524198224||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524134566||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00769910345||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524344258||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524278495||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524312437||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524083163||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524770333||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00829572188||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524396085||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00909212078||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524214908||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524150456||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524239498||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524095954||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00530094654||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm,deletion|intergenic_variant|MODIFIER||||||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|exit_rm;END=6707844;SVLEN=-14429;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:64802:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
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114
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4 106320294 . 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|0.985||pathogenic|0&0&1|1&1&1|27523597|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7474259||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|0.992||pathogenic|0&0&1|1&1&1|27523597|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.75460654||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|0&0&1|1&1&1|27523597|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.89774835||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|0.993||pathogenic|0&0&1|1&1&1|27523597|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.77676606||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001994744|promoter_flanking_region||||||||||rs138215926&CM1610192&COSV58994362|1|||||||||||||pathogenic|0&0&1|1&1&1|27523597||||||||||||||||||||||||||||||||||9.359000|4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:0,50:50:50:AD:1:27068:0:.:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 0|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|1:0,50:50:50:.:.:.:.:.:.
|
|
115
|
-
9 107546633 . 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|0.97944254|||||||LC|4.243||AD&AR||||||||||||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,10:10:.:AR:0:19:1:OK:GQ&DP&VIM&exit_u1 0|1:1,49:50:50:.:.:.:.:.:. 1|0:0,50:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
|
|
116
|
-
9 107584864 . AC A . PASS CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|19/50||NM_005502.4:c.2740del|NP_005493.2:p.Val914TrpfsTer8|3053/10408|2740/6786|914/2261|V/X|Gtg/tg||1||-1||1|EntrezGene|||||||||||||||||||33|-42|28|1|0.00|0.00|0.10|0.00|ABCA1|VUS|0.998016||||||HP:0000951|LC|4.243||AD&AR||LP||||4.010000||||||||LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:10,90:50:50:AD:1:19:1:OK:GQ&DP&VIM&exit_u1 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
|
|
117
|
-
9 107584865 . C G . PASS CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|19/50||NM_005502.4:c.2740del|NP_005493.2:p.Val914TrpfsTer8|3053/10408|2740/6786|914/2261|V/X|Gtg/tg||1||-1||1|EntrezGene|||||||||||||||||||33|-42|28|1|0.00|0.00|0.10|0.00|ABCA1|VUS|0.998016||||||HP:0003124|HC|4.243||AD&AR||LP||||4.010000||||||||LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:10,90:50:50:AD:1:19:1:OK:GQ&DP&VIM&exit_u1 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
|
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118
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10 126091499 . 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|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9327103||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98210585||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9327103||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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||1|EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97306395||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9656282||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96872944||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9635119||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97306395||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96748227||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96553046||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:4942:1:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
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119
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13 77570128 . 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|0.995||pathogenic||1||||||||194|-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.9957157||||||||1.166||AR||LP||||9.873000||||623394|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|0.999||pathogenic||1||||||||194|-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.99436617||||||||1.166||AR||LP||||9.873000||||623394|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:1:0:OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 1|1:0,50:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:.
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120
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14 89307838 . C T . PASS CSQ=T|stop_gained|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|6/16||NM_001288781.1:c.529C>T|NP_001275710.1:p.Gln177Ter|725/2378|529/1596|177/531|Q/*|Cag/Tag|rs376035653|1||1||1|EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9826843||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|5_prime_UTR_variant|MODIFIER|TTC8|123016|Transcript|NM_001288782.1|protein_coding|6/14||NM_001288782.1:c.-34C>T||725/2298|||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.007844023|0|1|17|uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GCCATGA&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:562&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAGATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:550&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:CAGATGC&uSTOP_gained_KozakStrength:Weak&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:475&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAAATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:412&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAAATGA&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:364&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:ATGATGC&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:361&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:ACTATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:190&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:TCCATGC&uSTOP_gained_KozakStrength:Weak&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:97&uSTOP_gained_ref_type:uORF|uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained|HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001288783.1|protein_coding||5/14|NM_001288783.1:c.-199+298C>T|||||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|5/13||NM_001366535.2:c.529C>T|NP_001353464.1:p.Gln177Ter|586/5160|529/1434|177/477|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9942367||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001366536.2|protein_coding||4/11|NM_001366536.2:c.459+298C>T|||||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|6/15||NM_144596.4:c.559C>T|NP_653197.2:p.Gln187Ter|616/2183|559/1548|187/515|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9777649||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|6/15||NM_198309.3:c.529C>T|NP_938051.1:p.Gln177Ter|725/2300|529/1518|177/505|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9769935||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_198310.3|protein_coding||5/13|NM_198310.3:c.459+298C>T|||||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|5/15||NR_159362.2:n.586C>T||586/5304|||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.0989985||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001864166|enhancer||||||||||rs376035653|1||||||||||||||||||||||||||||||||||||||||||||||||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|0:25,25:50:50:AD:1:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
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121
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14 89310195 . G A . PASS CSQ=A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding||7/15|NM_001288781.1:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1||1|EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001288782.1|protein_coding||6/13|NM_001288782.1:c.30+2294G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.8040881||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding||6/14|NM_001288783.1:c.-154+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding||6/12|NM_001366535.2:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding||5/11|NM_001366536.2:c.504+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding||7/14|NM_144596.4:c.624+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding||7/14|NM_198309.3:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding||6/13|NM_198310.3:c.504+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|splice_donor_variant&non_coding_transcript_variant|HIGH|TTC8|123016|Transcript|NR_159362.2|misc_RNA||6/14|NR_159362.2:n.651+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9901416||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp;VIPC_S=LQ GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,9:9:50:AR:0:123016:1:U3,U3,U3,U3,U3,U3,U3,U3,U3:GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3 0|1:.:10:50:.:.:.:.:.:. 0|1:50:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
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|
122
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-
14 89336407 . 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||1|EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9979407||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9975501||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9940432||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.99769527||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9988078||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.99404776||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9971411||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9968329||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.6298463||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:123016:1:OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
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|
123
|
-
14 105167860 . 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|0.9748948||||||||0.87||AD||LP||||7.817000||||||||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|0.97195035||||||||0.87||AD||LP||||7.817000||||||||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|0.97388726||||||||0.87||AD||LP||||7.817000||||||||LP|filter&vkgl&exit_lp,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001573054|open_chromatin_region|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||7.817000||||||||LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:0:OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 0|0:50,0:50:50:.:.:.:.:. 1|0:45,5:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
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|
124
|
-
17 29556064 . 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|0.9992588||||||HP:0000951||0.583|1|AD||LP||||4.630000||||||||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|0.99961036||||||HP:0000951||0.583|1|AD||LP||||4.630000||||||||LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:1:0:NOK,NOK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 1|1:0,50:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 1|0:25,25:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 1|0:25,25:50:50:.:.:.:.
|
|
125
|
-
17 29585422 . A G . PASS CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|31/57||NM_000267.3:c.4171A>G|NP_000258.1:p.Arg1391Gly|4554/12362|4171/8457|1391/2818|R/G|Aga/Gga|rs1555618515&CM1211610|1||1|||EntrezGene|||||0|0.962||pathogenic||1&1||||||||125|-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.9277154||||||HP:0000951||0.583|1|AD||LP||||4.149000||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|32/58||NM_001042492.3:c.4234A>G|NP_001035957.1:p.Arg1412Gly|4567/12373|4234/8520|1412/2839|R/G|Aga/Gga|rs1555618515&CM1211610|1||1||1|EntrezGene|||||0|0.988||pathogenic||1&1||||||||125|-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.97049046||||||HP:0000951||0.583|1|AD||LP||||4.149000||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:.:AR:1:0:OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 0|1:.:10:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
|
|
126
|
-
17 29663879 . 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|CM141499&CM143458|1||1|||EntrezGene|||||0|0.994||||1&1||||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.99390525||||||HP:0000951||0.583|1|AD||LP||||7.536000||||996527|Likely_pathogenic||criteria_provided&_single_submitter|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|CM141499&CM143458|1||1||1|EntrezGene|||||0|0.993||||1&1||||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.9962404||||||HP:0000951||0.583|1|AD||LP||||7.536000||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:25,25:50:50:AD_IP:0:4763:1:OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 0|0:50,0:50:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
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|
127
|
-
17 29683983 . C T . PASS CSQ=T|stop_gained|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|52/57||NM_000267.3:c.7681C>T|NP_000258.1:p.Gln2561Ter|8064/12362|7681/8457|2561/2818|Q/*|Cag/Tag|CM143479|1||1|||EntrezGene||||||||||1|||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.9976593||||||HP:0000951||0.583|1|AD||LP||||6.871000||||||||LP|filter&vkgl&exit_lp,T|stop_gained|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|53/58||NM_001042492.3:c.7744C>T|NP_001035957.1:p.Gln2582Ter|8077/12373|7744/8520|2582/2839|Q/*|Cag/Tag|CM143479|1||1||1|EntrezGene||||||||||1|||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.9986885||||||HP:0000951||0.583|1|AD||LP||||6.871000||||||||LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S:VIS .|.:25,25:50:50:AR,AD:0:4763:1:OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.
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128
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19 11224051 . C CGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAG . PASS CSQ=TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_000527.5|protein_coding|9/18||NM_000527.5:c.1289_1309dup|NP_000518.1:p.Val436_Ala437insGlyGlyArgSerGlyHisGly|1395-1396/5173|1309-1310/2583|437/860|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1||1|EntrezGene|||||||25|||||||||||||||||||||VUS|0.8812568|||||||HC|5.497||AD&AR||LP||||||||||||LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:.:10:50:AR:0:3949:1:OK:GQ&DP&VIM&exit_u1 0|1:.:10:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
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129
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-
19 17449399 . C T . PASS CSQ=T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_001128855.3|protein_coding|4/9||NM_001128855.3:c.440C>T|NP_001122327.1:p.Ala147Val|499/2503|440/1416|147/471|A/V|gCg/gTg|rs774708853&COSV50176281|1||1|||EntrezGene|||||0|0.999||likely_pathogenic|0&1|1&1||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.92324424||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp,T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_001195422.1|protein_coding|4/9||NM_001195422.1:c.506C>T|NP_001182351.1:p.Ala169Val|528/2595|506/1545|169/514|A/V|gCg/gTg|rs774708853&COSV50176281|1||1|||EntrezGene|||||0|0.997||likely_pathogenic|0&1|1&1||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.65621275||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp,T|upstream_gene_variant|MODIFIER|ANO8|57719|Transcript|NM_020959.3|protein_coding||||||||||rs774708853&COSV50176281|1|3735|-1|||EntrezGene||||||||likely_pathogenic|0&1|1&1|||||||||-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.71450377||||||||-1.785||||||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_032620.4|protein_coding|4/9||NM_032620.4:c.440C>T|NP_116009.2:p.Ala147Val|499/2566|440/1479|147/492|A/V|gCg/gTg|rs774708853&COSV50176281|1||1|||EntrezGene|||||0|0.999||likely_pathogenic|0&1|1&1||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.84315056||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp,T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_133644.4|protein_coding|4/8||NM_133644.4:c.440C>T|NP_598399.2:p.Ala147Val|499/2662|440/1575|147/524|A/V|gCg/gTg|rs774708853&COSV50176281|1||1||1|EntrezGene|||||0|0.999||likely_pathogenic|0&1|1&1||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.8864299||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000107883|promoter||||||||||rs774708853&COSV50176281|1|||||||||||||likely_pathogenic|0&1|1&1|||||||||||||||||||||||||||||||||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|0:25,25:50:50:AD:1:0:OK,OK,OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
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130
|
-
19 17451997 . 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||1||1|||EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.99768054||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||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||1||1|||EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.99091107||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||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||1||1|||EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.99607384||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||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||1||1||1|EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.9972447||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||LP|filter&vkgl&exit_lp,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001610216|CTCF_binding_site|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||5.586000||||||||LQ|exit_rm,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001909308|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||5.586000||||||||LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523665928||||||||||||1||1||||||||||||||||ENSPFM0305|8|N||HOXB2::ELF1||||||||||||||||||||||||||||5.586000||||||||LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:84705:1:OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 0|0:10,0:10:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 1|1:0,50:50:50:.:.:.:.:.:. 1|1:0,50:50:50:.:.:.:.:.:.
|
|
131
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-
22 50721546 . C T . PASS CSQ=T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376864.1|protein_coding|17/37||NM_001376864.1:c.2749G>A|NP_001363793.1:p.Gly917Ser|2881/6611|2749/5754|917/1917|G/S|Ggc/Agc|rs1377653283|1||-1||1|EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14641568||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376865.1|protein_coding|18/38||NM_001376865.1:c.2818G>A|NP_001363794.1:p.Gly940Ser|2898/6391|2818/5586|940/1861|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.10027899||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376866.1|protein_coding|17/37||NM_001376866.1:c.2749G>A|NP_001363795.1:p.Gly917Ser|2909/6402|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.71265084||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376867.1|protein_coding|18/38||NM_001376867.1:c.2749G>A|NP_001363796.1:p.Gly917Ser|2969/6462|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376868.1|protein_coding|18/38||NM_001376868.1:c.2749G>A|NP_001363797.1:p.Gly917Ser|2962/6455|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376869.1|protein_coding|16/36||NM_001376869.1:c.2749G>A|NP_001363798.1:p.Gly917Ser|2856/6349|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.66974294||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376870.1|protein_coding|17/37||NM_001376870.1:c.2749G>A|NP_001363799.1:p.Gly917Ser|2881/6374|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.6837599||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376871.1|protein_coding|17/37||NM_001376871.1:c.2749G>A|NP_001363800.1:p.Gly917Ser|2874/6367|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.6837599||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376872.1|protein_coding|19/39||NM_001376872.1:c.2749G>A|NP_001363801.1:p.Gly917Ser|3066/6559|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7025085||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376873.1|protein_coding|18/38||NM_001376873.1:c.2749G>A|NP_001363802.1:p.Gly917Ser|3218/6711|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7267535||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376874.1|protein_coding|18/38||NM_001376874.1:c.2749G>A|NP_001363803.1:p.Gly917Ser|2934/6427|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376875.1|protein_coding|16/36||NM_001376875.1:c.2749G>A|NP_001363804.1:p.Gly917Ser|2933/6426|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376876.1|protein_coding|18/38||NM_001376876.1:c.2749G>A|NP_001363805.1:p.Gly917Ser|2927/6420|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376877.1|protein_coding|18/38||NM_001376877.1:c.2749G>A|NP_001363806.1:p.Gly917Ser|3198/6691|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.70509267||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376878.1|protein_coding|16/36||NM_001376878.1:c.2749G>A|NP_001363807.1:p.Gly917Ser|2821/6314|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.66974294||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376879.1|protein_coding|19/39||NM_001376879.1:c.2749G>A|NP_001363808.1:p.Gly917Ser|3101/6594|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.69429386||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376880.1|protein_coding|17/37||NM_001376880.1:c.2749G>A|NP_001363809.1:p.Gly917Ser|2991/6484|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376881.1|protein_coding|18/38||NM_001376881.1:c.2749G>A|NP_001363810.1:p.Gly917Ser|3046/6539|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.8251113||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376882.1|protein_coding|17/37||NM_001376882.1:c.2749G>A|NP_001363811.1:p.Gly917Ser|3165/6658|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.70509267||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376883.1|protein_coding|17/37||NM_001376883.1:c.2749G>A|NP_001363812.1:p.Gly917Ser|2881/6350|2749/5493|917/1830|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.10285367||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376884.1|protein_coding|16/36||NM_001376884.1:c.2749G>A|NP_001363813.1:p.Gly917Ser|2821/6236|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.119815774||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376885.1|protein_coding|17/37||NM_001376885.1:c.2749G>A|NP_001363814.1:p.Gly917Ser|2909/6324|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.114952855||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376886.1|protein_coding|17/37||NM_001376886.1:c.2656G>A|NP_001363815.1:p.Gly886Ser|2876/6369|2656/5424|886/1807|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.12163515||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_012401.4|protein_coding|17/37||NM_012401.4:c.2749G>A|NP_036533.2:p.Gly917Ser|2916/6409|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.75893486||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001960812|promoter||||||||||rs1377653283|1||||||||||||||||||||||||||||||||||||||||||||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:.:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 0|0:10,0:10:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
|
|
132
|
-
22 51224051 . G A . PASS CSQ=A|missense_variant|MODERATE|FAKE|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||0|1||likely_pathogenic|0&0&0&1|1&1&1&1||||||||180|28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.9769107||||||HP:0000951||2.452||AD&AR||LP||||9.093000||||183735|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:AR:1:6390:1:OK:VIM&exit_u1 1|0:45,5:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:. 1|0:25,25:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:.
|
|
133
|
-
X 48933021 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|||EntrezGene||||||||||1|||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9742088||||||HP:0000951||1.088||XL||LP||||8.134000||||||||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||1|EntrezGene||||||||||1|||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9742088||||||HP:0000951||1.088||XL||LP||||8.134000||||||||LP|filter&vkgl&exit_lp,T|upstream_gene_variant|MODIFIER|PRAF2|11230|Transcript|NM_007213.3|protein_coding||||||||||CS135341|1|1360|-1|||EntrezGene||||||||||1|||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.7629854||||||||-0.375||||||||8.134000||||||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001477865|CTCF_binding_site||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||||||||8.134000||||||||LQ|exit_rm,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001765299|promoter_flanking_region||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||||||||8.134000||||||||LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VID:VIM:VIPC_S:VIPP_S 1|0:25,25:50:50:1:0:OK,OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 1|0:25,25:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 1|1:0,50:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 1|1:0,50:50:50:.:.:.:.
|
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134
|
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Y 2655641 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||1&1|2401216&9443877||||||||-26|-50|2|-4|0.01|0.00|0.00|0.00|SRY|VUS|0.85415643||||||||2.02||||||||0.170000||||9753|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&clinVar&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VID:VIM:VIPC_S:VIPP_S 1:50:50:50:1:0:OK:GQ&DP&VIM&VID&exit_u1 0:.:10:50:.:.:.:. .:.:.:50:.:.:.:. .:.:.:50:.:.:.:. 1:50:50:50:.:.:.:. 1:50:50:50:.:.:.:.
|