{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA116465", "communityStandardTitle": [ "NM_000081.4(LYST):c.5996T>A (p.Val1999Asp)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=18856[alleleid]", "alleleId": 18856, "preferredName": "NM_000081.4(LYST):c.5996T>A (p.Val1999Asp)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/3817", "RCV": [ "RCV000004021", "RCV000055738" ], "variationId": 3817 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235929504A>T?assembly=hg19", "id": "chr1:g.235929504A>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235766204A>T?assembly=hg38", "id": "chr1:g.235766204A>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/28942077", "rs": 28942077 } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 235766204, "referenceAllele": "A", "start": 235766203 } ], "hgvs": [ "NC_000001.11:g.235766204A>T", "CM000663.2:g.235766204A>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 235929504, "referenceAllele": "A", "start": 235929503 } ], "hgvs": [ "NC_000001.10:g.235929504A>T", "CM000663.1:g.235929504A>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 233996127, "referenceAllele": "A", "start": 233996126 } ], "hgvs": [ "NC_000001.9:g.233996127A>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "A", "end": 122437, "referenceAllele": "T", "start": 122436 } ], "hgvs": [ "NG_007397.1:g.122437T>A", "LRG_143:g.122437T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000565" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 671, "referenceAllele": "T", "start": 670 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000461526.2:c.671T>A" ], "proteinEffect": { "hgvs": "ENSP00000513165.1:p.Val224Asp", "hgvsWellDefined": "ENSP00000513165.1:p.Val224Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS905084" }, { "coordinates": [ { "allele": "A", "end": 6052, "referenceAllele": "T", "start": 6051 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697178.1:c.*1420T>A" ], "proteinEffect": { "hgvs": "ENSP00000513163.1:n.*1420T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS908583" }, { "coordinates": [ { "allele": "A", "end": 557, "endIntronDirection": "+", "endIntronOffset": 35, "referenceAllele": "T", "start": 557, "startIntronDirection": "+", "startIntronOffset": 34 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697180.1:c.557+35T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS908585" }, { "coordinates": [ { "allele": "A", "end": 428, "referenceAllele": "T", "start": 427 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697241.1:c.428T>A" ], "proteinEffect": { "hgvs": "ENSP00000513206.1:p.Val143Asp", "hgvsWellDefined": "ENSP00000513206.1:p.Val143Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS908629" }, { "coordinates": [ { "allele": "A", "end": 6157, "referenceAllele": "T", "start": 6156 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.7:c.5996T>A" ], "proteinEffect": { "hgvs": "ENSP00000374443.2:p.Val1999Asp", "hgvsWellDefined": "ENSP00000374443.2:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS752840", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.5996T>A" }, "RefSeq": { "hgvs": "NM_000081.4:c.5996T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Val1999Asp" }, "RefSeq": { "hgvs": "NP_000072.2:p.Val1999Asp" } } } }, { "coordinates": [ { "allele": "A", "end": 6171, "referenceAllele": "T", "start": 6170 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.6:c.5996T>A" ], "proteinEffect": { "hgvs": "ENSP00000374443.2:p.Val1999Asp", "hgvsWellDefined": "ENSP00000374443.2:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS274290" }, { "coordinates": [ { "allele": "A", "end": 5748, "referenceAllele": "T", "start": 5747 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389794.7:c.*1420T>A" ], "proteinEffect": { "hgvs": "ENSP00000374444.4:n.*1420T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS274291" }, { "coordinates": [ { "allele": "A", "end": 6512, "endIntronDirection": "+", "endIntronOffset": 35, "referenceAllele": "T", "start": 6512, "startIntronDirection": "+", "startIntronOffset": 34 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000489585.5:n.6512+35T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS327618" }, { "@id": "http://reg.genome.network/allele/PA097826", "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_000081.3:c.5996T>A", "LRG_143t1:c.5996T>A" ], "proteinEffect": { "hgvs": "NP_000072.2:p.Val1999Asp", "hgvsWellDefined": "NP_000072.2:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS006145" }, { "@id": "http://reg.genome.network/allele/PA116468", "coordinates": [ { "allele": "A", "end": 6615, "referenceAllele": "T", "start": 6614 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_001301365.1:c.5996T>A", "LRG_143t2:c.5996T>A" ], "proteinEffect": { "hgvs": "NP_001288294.1:p.Val1999Asp", "hgvsWellDefined": "NP_001288294.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS025192" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544031.1:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542333.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542333.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS110944" }, { "coordinates": [ { "allele": "A", "end": 6581, "referenceAllele": "T", "start": 6580 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544032.1:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542334.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542334.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS110945" }, { "coordinates": [ { "allele": "A", "end": 6379, "referenceAllele": "T", "start": 6378 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.1:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542335.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS110946" }, { "coordinates": [ { "allele": "A", "end": 6040, "referenceAllele": "T", "start": 6039 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544034.1:c.5858T>A" ], "proteinEffect": { "hgvs": "XP_011542336.1:p.Val1953Asp", "hgvsWellDefined": "XP_011542336.1:p.Val1953Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS110947" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544035.1:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542337.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542337.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS110948" }, { "coordinates": [ { "allele": "A", "end": 3823, "referenceAllele": "T", "start": 3822 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544036.1:c.3659T>A" ], "proteinEffect": { "hgvs": "XP_011542338.1:p.Val1220Asp", "hgvsWellDefined": "XP_011542338.1:p.Val1220Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS110949" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544037.1:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542339.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542339.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS110950" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544038.1:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542340.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542340.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS110951" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544039.1:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542341.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542341.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS110952" }, { "coordinates": [ { "allele": "A", "end": 6143, "endIntronDirection": "+", "endIntronOffset": 35, "referenceAllele": "T", "start": 6143, "startIntronDirection": "+", "startIntronOffset": 34 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544040.1:c.5961+35T>A" ], "proteinEffect": { "hgvs": "XP_011542342.1:n.5961+35T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS110953" }, { "coordinates": [ { "allele": "A", "end": 6328, "referenceAllele": "T", "start": 6327 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.2:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542335.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS555477" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544035.2:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542337.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542337.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS555478" }, { "coordinates": [ { "allele": "A", "end": 3832, "referenceAllele": "T", "start": 3831 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544036.2:c.3659T>A" ], "proteinEffect": { "hgvs": "XP_011542338.1:p.Val1220Asp", "hgvsWellDefined": "XP_011542338.1:p.Val1220Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS555479" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544037.2:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542339.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542339.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS555480" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544039.2:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_011542341.1:p.Val1999Asp", "hgvsWellDefined": "XP_011542341.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS555481" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_017000150.1:c.5996T>A" ], "proteinEffect": { "hgvs": "XP_016855639.1:p.Val1999Asp", "hgvsWellDefined": "XP_016855639.1:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS556567" }, { "coordinates": [ { "allele": "A", "end": 6005, "endIntronDirection": "+", "endIntronOffset": 35, "referenceAllele": "T", "start": 6005, "startIntronDirection": "+", "startIntronOffset": 34 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_017000151.1:c.5823+35T>A" ], "proteinEffect": { "hgvs": "XP_016855640.1:n.5823+35T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS556568" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736946.2:n.6178T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS587794" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736947.1:n.6178T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS587795" }, { "coordinates": [ { "allele": "A", "end": 6178, "referenceAllele": "T", "start": 6177 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736948.1:n.6178T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS587796" }, { "coordinates": [ { "allele": "A", "end": 6143, "endIntronDirection": "+", "endIntronOffset": 35, "referenceAllele": "T", "start": 6143, "startIntronDirection": "+", "startIntronOffset": 34 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_002959252.1:n.6143+35T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS605185" }, { "@id": "http://reg.genome.network/allele/PA097826", "coordinates": [ { "allele": "A", "end": 6157, "referenceAllele": "T", "start": 6156 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_000081.4:c.5996T>A" ], "proteinEffect": { "hgvs": "NP_000072.2:p.Val1999Asp", "hgvsWellDefined": "NP_000072.2:p.Val1999Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS674690", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.5996T>A" }, "RefSeq": { "hgvs": "NM_000081.4:c.5996T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Val1999Asp" }, "RefSeq": { "hgvs": "NP_000072.2:p.Val1999Asp" } } } } ], "type": "nucleotide" }