{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA344943103", "communityStandardTitle": [ "NM_000081.4(LYST):c.6283C>T (p.Gln2095Ter)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1407913[alleleid]", "alleleId": 1407913, "preferredName": "NM_000081.4(LYST):c.6283C>T (p.Gln2095Ter)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/1378721", "RCV": [ "RCV001881298" ], "variationId": 1378721 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235922870G>A?assembly=hg19", "id": "chr1:g.235922870G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235759570G>A?assembly=hg38", "id": "chr1:g.235759570G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1667380258", "rs": 1667380258 } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-235759570-G-A?dataset=gnomad_r4", "id": "1-235759570-G-A", "variant": "1:235759570 G / A" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "A", "end": 235759570, "referenceAllele": "G", "start": 235759569 } ], "hgvs": [ "NC_000001.11:g.235759570G>A", "CM000663.2:g.235759570G>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "A", "end": 235922870, "referenceAllele": "G", "start": 235922869 } ], "hgvs": [ "NC_000001.10:g.235922870G>A", "CM000663.1:g.235922870G>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "A", "end": 233989493, "referenceAllele": "G", "start": 233989492 } ], "hgvs": [ "NC_000001.9:g.233989493G>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "T", "end": 129071, "referenceAllele": "C", "start": 129070 } ], "hgvs": [ "NG_007397.1:g.129071C>T", "LRG_143:g.129071C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS000565" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "T", "end": 958, "referenceAllele": "C", "start": 957 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000461526.2:c.958C>T" ], "proteinEffect": { "hgvs": "ENSP00000513165.1:p.Gln320Ter", "hgvsWellDefined": 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"ENSP00000513206.1:p.Gln239Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS908629" }, { "coordinates": [ { "allele": "T", "end": 6444, "referenceAllele": "C", "start": 6443 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.7:c.6283C>T" ], "proteinEffect": { "hgvs": "ENSP00000374443.2:p.Gln2095Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS752840", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.6283C>T" }, "RefSeq": { "hgvs": "NM_000081.4:c.6283C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Gln2095Ter" }, "RefSeq": { "hgvs": "NP_000072.2:p.Gln2095Ter" } } } }, { "coordinates": [ { "allele": "T", "end": 6458, "referenceAllele": "C", "start": 6457 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.6:c.6283C>T" ], 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"gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544032.1:c.6283C>T" ], "proteinEffect": { "hgvs": "XP_011542334.1:p.Gln2095Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS110945" }, { "coordinates": [ { "allele": "T", "end": 6666, "referenceAllele": "C", "start": 6665 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.1:c.6283C>T" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Gln2095Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS110946" }, { "coordinates": [ { "allele": "T", "end": 6327, "referenceAllele": "C", "start": 6326 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544034.1:c.6145C>T" ], "proteinEffect": { "hgvs": "XP_011542336.1:p.Gln2049Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS110947" }, { "coordinates": [ { "allele": "T", "end": 6465, "referenceAllele": "C", "start": 6464 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544035.1:c.6283C>T" ], "proteinEffect": { "hgvs": "XP_011542337.1:p.Gln2095Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS110948" }, { "coordinates": [ { "allele": "T", "end": 4110, "referenceAllele": "C", "start": 4109 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544036.1:c.3946C>T" ], "proteinEffect": { "hgvs": "XP_011542338.1:p.Gln1316Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS110949" }, { "coordinates": [ { "allele": "T", "end": 6465, "referenceAllele": "C", "start": 6464 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544037.1:c.6283C>T" ], "proteinEffect": { "hgvs": "XP_011542339.1:p.Gln2095Ter", "hgvsWellDefined": "XP_011542339.1:p.Gln2095_His2876delinsMetAlaAlaHisMetLeuArgSerArgSerLeuProAlaPheProThrSerSerLeuLeuThrGlnSerGlnLysLeuThrGlySerLeuGlyCysSerIleAspArgLeuGlnAsnIleAlaAspThrTyrValAlaThrGlnSerLysLysGlnAsnSerLeuGlySerSerAspThrLeuLysLysGlyLysGluAspAlaPheIleSerSerCysGluSerAlaLysThrValCysGluMetGluAlaValLeuSerAlaGlnValSerValSerAspValProLysGlyValLeuGlyPheProValValLysAlaAspHisLysGlnLeuGlyAlaGluProArgSerGluAspAspSerProGlyAspGluSerCysProArgArgProAspTyrLeuLysGlyLeuAlaSerPheGlnArgSerHisSerThrIleAlaSerLeuGlyLeuAlaPheProSerGlnAsnGlySerAlaAlaValGlyArgTrpProSerLeuValAspArgAsnThrAspAspTrpGluAsnPheAlaTyrSerLeuGlyTyrGluProAsnTyrAsnArgThrAlaSerAlaHisSerValThrGluAspCysLeuValProIleCysCysGlyLeuTyrGluLeuLeuSerGlyValLeuLeuIleLeuProAspValLeuLeuGluAspValMetAspLysLeuIleGlnAlaAspThrLeuLeuValLeuValAsnHisProSerProAlaIleGlnGlnGlyValIleLysLeuLeuAspAlaTyrPheAlaArgAlaSerLysGluGlnLysAspLysPheLeuLysAsnArgGlyPheSerLeuLeuAlaAsnGlnLeuTyrLeuHisArgGlyThrGlnGluLeuLeuGluCysPheIleGluMetPhePheGlyArgHisIleGlyLeuAspGluGluPheAspLeuGluAspValArgAsnMetGlyLeuPheGlnLysTrpSerValIleProIleLeuGlyLeuIleGluThrSerLeuTyrAspAsnIleLeuLeuHisAsnAlaLeuLeuLeuLeuLeuGlnIleLeuAsnSerCysSerLysValAlaAspMetLeuLeuAspAsnGlyLeuLeuTyrValLeuCysAsnThrValAlaAlaLeuAsnGlyLeuGluLysAsnIleProMetSerGluTyrLysLeuLeuAlaCysAspIleGlnGlnLeuPheIleAlaValThrIleHisAlaCysSerSerSerGlySerGlnTyrPheArgValIleGluAspLeuIleValMetLeuGlyTyrLeuGlnAsnSerLysAsnLysArgThrGlnAsnMetAlaValAlaLeuGlnLeuArgValLeuGlnAlaAlaMetGluPheIleArgThrThrAlaAsnHisAspSerGluAsnLeuThrAspSerLeuGlnSerProSerAlaProHisHisAlaValValGlnLysArgLysSerIleAlaGlySerIleProMetLysGlySerIleIleProHisLeuProArgHisHisPheGlySerTyrGlyGlnLeuProMetProPheSerPheGlyProLeuAsnGlnAspSerSerProGlnPheSerProGlyCysThrThrCysValValProProGlyAlaGlyProArgLysPheProLeuAlaGlnThrGluSerLeuLeuMetLysMetArgSerValAlaAsnAspGluLeuHisValMetMetGlnArgArgMetSerGlnGluAsnProSerGlnAlaThrGluThrGluLeuAlaGlnArgLeuGlnArgLeuThrValLeuAlaValAsnArgIleIleTyrGlnGluPheAsnSerAspIleIleAspIleLeuArgThrProGluAsnValThrGlnSerLysThrSerValPheGlnThrGluIleSerGluGluAsnIleHisHisGluGlnSerSerValPheAsnProPheGlnLysGluIlePheThrTyrLeuValGluGlyPheLysValSerIleGlySerSerLysAlaSerGlySerLysGlnGlnTrpThrLysIleLeuTrpSerCysLysGluThrPheArgMetGlnLeuGlyArgLeuLeuValHisIleLeuSerProAlaHisAlaAlaGlnGluArgLysGlnIlePheGluIleValHisGluProAsnHisGlnGluIleLeuArgAspCysLeuSerProSerLeuGlnArgGluIleCysIleAspTyrSerThrAlaProTyrArgLeuLeuTyrSerSerLysLysGluGlnThrThrGlyThrSerThrIleMetAspGluSerGlnLysHisTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS110950" }, { "coordinates": [ { "allele": "T", "end": 6465, "referenceAllele": "C", "start": 6464 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544038.1:c.6283C>T" ], "proteinEffect": { "hgvs": "XP_011542340.1:p.Gln2095Ter", "hgvsWellDefined": "XP_011542340.1:p.Gln2095_His2842delinsMetAlaAlaHisMetLeuArgSerArgSerLeuProAlaPheProThrSerSerLeuLeuThrGlnSerGlnLysLeuThrGlySerLeuGlyCysSerIleAspArgLeuGlnAsnIleAlaAspThrTyrValAlaThrGlnSerLysLysGlnAsnSerLeuGlySerSerAspThrLeuLysLysGlyLysGluAspAlaPheIleSerSerCysGluSerAlaLysThrValCysGluMetGluAlaValLeuSerAlaGlnValSerValSerAspValProLysGlyValLeuGlyPheProValValLysAlaAspHisLysGlnLeuGlyAlaGluProArgSerGluAspAspSerProGlyAspGluSerCysProArgArgProAspTyrLeuLysGlyLeuAlaSerPheGlnArgSerHisSerThrIleAlaSerLeuGlyLeuAlaPheProSerGlnAsnGlySerAlaAlaValGlyArgTrpProSerLeuValAspArgAsnThrAspAspTrpGluAsnPheAlaTyrSerLeuGlyTyrGluProAsnTyrAsnArgThrAlaSerAlaHisSerValThrGluAspCysLeuValProIleCysCysGlyLeuTyrGluLeuLeuSerGlyValLeuLeuIleLeuProAspValLeuLeuGluAspValMetAspLysLeuIleGlnAlaAspThrLeuLeuValLeuValAsnHisProSerProAlaIleGlnGlnGlyValIleLysLeuLeuAspAlaTyrPheAlaArgAlaSerLysGluGlnLysAspLysPheLeuLysAsnArgGlyPheSerLeuLeuAlaAsnGlnLeuTyrLeuHisArgGlyThrGlnGluLeuLeuGluCysPheIleGluMetPhePheGlyArgHisIleGlyLeuAspGluGluPheAspLeuGluAspValArgAsnMetGlyLeuPheGlnLysTrpSerValIleProIleLeuGlyLeuIleGluThrSerLeuTyrAspAsnIleLeuLeuHisAsnAlaLeuLeuLeuLeuLeuGlnIleLeuAsnSerCysSerLysValAlaAspMetLeuLeuAspAsnGlyLeuLeuTyrValLeuCysAsnThrValAlaAlaLeuAsnGlyLeuGluLysAsnIleProMetSerGluTyrLysLeuLeuAlaCysAspIleGlnGlnLeuPheIleAlaValThrIleHisAlaCysSerSerSerGlySerGlnTyrPheArgValIleGluAspLeuIleValMetLeuGlyTyrLeuGlnAsnSerLysAsnLysArgThrGlnAsnMetAlaValAlaLeuGlnLeuArgValLeuGlnAlaAlaMetGluPheIleArgThrThrAlaAsnHisAspSerGluAsnLeuThrAspSerLeuGlnSerProSerAlaProHisHisAlaValValGlnLysArgLysSerIleAlaGlySerIleProMetLysGlySerIleIleProHisLeuProArgHisHisPheGlySerTyrGlyGlnLeuProMetProPheSerPheGlyProLeuAsnGlnAspSerSerProGlnPheSerProGlyCysThrThrCysValValProProGlyAlaGlyProArgLysPheProLeuAlaGlnThrGluSerLeuLeuMetLysMetArgSerValAlaAsnAspGluLeuHisValMetMetGlnArgArgMetSerGlnGluAsnProSerGlnAlaThrGluThrGluLeuAlaGlnArgLeuGlnArgLeuThrValLeuAlaValAsnArgIleIleTyrGlnGluPheAsnSerAspIleIleAspIleLeuArgThrProGluAsnValThrGlnSerLysThrSerValPheGlnThrGluIleSerGluGluAsnIleHisHisGluGlnSerSerValPheAsnProPheGlnLysGluIlePheThrTyrLeuValGluGlyPheLysValSerIleGlySerSerLysAlaSerGlySerLysGlnGlnTrpThrLysIleLeuTrpSerCysLysGluThrPheArgMetGlnLeuGlyArgLeuLeuValHisIleLeuSerProAlaHisAlaAlaGlnGluArgLysGlnIlePheGluIleValHisGluProAsnHisGlnGluIleLeuArgAspCysLeuSerProSerLeuGlnAlaHisTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS110951" }, { "coordinates": [ { "allele": "T", "end": 6465, "referenceAllele": "C", "start": 6464 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544039.1:c.6283C>T" ], "proteinEffect": { "hgvs": "XP_011542341.1:p.Gln2095Ter", "hgvsWellDefined": "XP_011542341.1:p.Gln2095_Ala2555delinsMetAlaAlaHisMetLeuArgSerArgSerLeuProAlaPheProThrSerSerLeuLeuThrGlnSerGlnLysLeuThrGlySerLeuGlyCysSerIleAspArgLeuGlnAsnIleAlaAspThrTyrValAlaThrGlnSerLysLysGlnAsnSerLeuGlySerSerAspThrLeuLysLysGlyLysGluAspAlaPheIleSerSerCysGluSerAlaLysThrValCysGluMetGluAlaValLeuSerAlaGlnValSerValSerAspValProLysGlyValLeuGlyPheProValValLysAlaAspHisLysGlnLeuGlyAlaGluProArgSerGluAspAspSerProGlyAspGluSerCysProArgArgProAspTyrLeuLysGlyLeuAlaSerPheGlnArgSerHisSerThrIleAlaSerLeuGlyLeuAlaPheProSerGlnAsnGlySerAlaAlaValGlyArgTrpProSerLeuValAspArgAsnThrAspAspTrpGluAsnPheAlaTyrSerLeuGlyTyrGluProAsnTyrAsnArgThrAlaSerAlaHisSerValThrGluAspCysLeuValProIleCysCysGlyLeuTyrGluLeuLeuSerGlyValLeuLeuIleLeuProAspValLeuLeuGluAspValMetAspLysLeuIleGlnAlaAspThrLeuLeuValLeuValAsnHisProSerProAlaIleGlnGlnGlyValIleLysLeuLeuAspAlaTyrPheAlaArgAlaSerLysGluGlnLysAspLysPheLeuLysAsnArgGlyPheSerLeuLeuAlaAsnGlnLeuTyrLeuHisArgGlyThrGlnGluLeuLeuGluCysPheIleGluMetPhePheGlyArgHisIleGlyLeuAspGluGluPheAspLeuGluAspValArgAsnMetGlyLeuPheGlnLysTrpSerValIleProIleLeuGlyLeuIleGluThrSerLeuTyrAspAsnIleLeuLeuHisAsnAlaLeuLeuLeuLeuLeuGlnIleLeuAsnSerCysSerLysValAlaAspMetLeuLeuAspAsnGlyLeuLeuTyrValLeuCysAsnThrValAlaAlaLeuAsnGlyLeuGluLysAsnIleProMetSerGluTyrLysLeuLeuAlaCysAspIleGlnGlnLeuPheIleAlaValThrIleHisAlaCysSerSerSerGlySerGlnTyrPheArgValIleGluAspLeuIleValMetLeuGlyTyrLeuGlnAsnSerLysAsnLysArgThrGlnIleSerSerValPheArgTyrGlyCysCysThrThrAlaTer" 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