{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA1466433", "communityStandardTitle": [ "NM_000081.4(LYST):c.6158T>C (p.Met2053Thr)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=2413188[alleleid]", "alleleId": 2413188, "preferredName": "NM_000081.4(LYST):c.6158T>C (p.Met2053Thr)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/2433556", "RCV": [ "RCV003131523" ], "variationId": 2433556 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/1-235926115-A-G", "id": "1-235926115-A-G", "variant": "1:235926115 A / G" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235926115A>G?assembly=hg19", "id": "chr1:g.235926115A>G" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235762815A>G?assembly=hg38", "id": "chr1:g.235762815A>G" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/768532041", "rs": 768532041 } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-235762815-A-G?dataset=gnomad_r4", "id": "1-235762815-A-G", "variant": "1:235762815 A / G" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "G", "end": 235762815, "referenceAllele": "A", "start": 235762814 } ], "hgvs": [ "NC_000001.11:g.235762815A>G", "CM000663.2:g.235762815A>G" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "G", "end": 235926115, "referenceAllele": "A", "start": 235926114 } ], "hgvs": [ "NC_000001.10:g.235926115A>G", "CM000663.1:g.235926115A>G" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "G", "end": 233992738, "referenceAllele": "A", "start": 233992737 } ], "hgvs": [ "NC_000001.9:g.233992738A>G" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "C", "end": 125826, "referenceAllele": "T", "start": 125825 } ], "hgvs": [ "NG_007397.1:g.125826T>C", "LRG_143:g.125826T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS000565" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "C", "end": 833, "referenceAllele": "T", "start": 832 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000461526.2:c.833T>C" ], "proteinEffect": { "hgvs": "ENSP00000513165.1:p.Met278Thr", "hgvsWellDefined": "ENSP00000513165.1:p.Met278Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS905084" }, { "coordinates": [ { "allele": "C", "end": 6214, "referenceAllele": "T", "start": 6213 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697178.1:c.*1582T>C" ], "proteinEffect": { "hgvs": "ENSP00000513163.1:n.*1582T>C" }, "referenceSequence": "http://reg.genome.network/refseq/RS908583" }, { "coordinates": [ { "allele": "C", "end": 663, "referenceAllele": "T", "start": 662 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697180.1:c.663T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS908585" }, { "coordinates": [ { "allele": "C", "end": 590, "referenceAllele": "T", "start": 589 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697241.1:c.590T>C" ], "proteinEffect": { "hgvs": "ENSP00000513206.1:p.Met197Thr", "hgvsWellDefined": "ENSP00000513206.1:p.Met197Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS908629" }, { "coordinates": [ { "allele": "C", "end": 6319, "referenceAllele": "T", "start": 6318 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.7:c.6158T>C" ], "proteinEffect": { "hgvs": "ENSP00000374443.2:p.Met2053Thr", "hgvsWellDefined": "ENSP00000374443.2:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS752840", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.6158T>C" }, "RefSeq": { "hgvs": "NM_000081.4:c.6158T>C" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Met2053Thr" }, "RefSeq": { "hgvs": "NP_000072.2:p.Met2053Thr" } } } }, { "coordinates": [ { "allele": "C", "end": 6333, "referenceAllele": "T", "start": 6332 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.6:c.6158T>C" ], "proteinEffect": { "hgvs": "ENSP00000374443.2:p.Met2053Thr", "hgvsWellDefined": "ENSP00000374443.2:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS274290" }, { "coordinates": [ { "allele": "C", "end": 5910, "referenceAllele": "T", "start": 5909 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389794.7:c.*1582T>C" ], "proteinEffect": { "hgvs": "ENSP00000374444.4:n.*1582T>C" }, "referenceSequence": "http://reg.genome.network/refseq/RS274291" }, { "coordinates": [ { "allele": "C", "end": 6549, "referenceAllele": "T", "start": 6548 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000489585.5:n.6549T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS327618" }, { "@id": "http://reg.genome.network/allele/PA2825049281", "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_000081.3:c.6158T>C", "LRG_143t1:c.6158T>C" ], "proteinEffect": { "hgvs": "NP_000072.2:p.Met2053Thr", "hgvsWellDefined": "NP_000072.2:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS006145" }, { "@id": "http://reg.genome.network/allele/PA2580191643", "coordinates": [ { "allele": "C", "end": 6777, "referenceAllele": "T", "start": 6776 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_001301365.1:c.6158T>C", "LRG_143t2:c.6158T>C" ], "proteinEffect": { "hgvs": "NP_001288294.1:p.Met2053Thr", "hgvsWellDefined": "NP_001288294.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS025192" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544031.1:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542333.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542333.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS110944" }, { "coordinates": [ { "allele": "C", "end": 6743, "referenceAllele": "T", "start": 6742 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544032.1:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542334.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542334.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS110945" }, { "coordinates": [ { "allele": "C", "end": 6541, "referenceAllele": "T", "start": 6540 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.1:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542335.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS110946" }, { "coordinates": [ { "allele": "C", "end": 6202, "referenceAllele": "T", "start": 6201 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544034.1:c.6020T>C" ], "proteinEffect": { "hgvs": "XP_011542336.1:p.Met2007Thr", "hgvsWellDefined": "XP_011542336.1:p.Met2007Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS110947" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544035.1:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542337.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542337.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS110948" }, { "coordinates": [ { "allele": "C", "end": 3985, "referenceAllele": "T", "start": 3984 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544036.1:c.3821T>C" ], "proteinEffect": { "hgvs": "XP_011542338.1:p.Met1274Thr", "hgvsWellDefined": "XP_011542338.1:p.Met1274Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS110949" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544037.1:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542339.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542339.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS110950" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544038.1:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542340.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542340.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS110951" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544039.1:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542341.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542341.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS110952" }, { "coordinates": [ { "allele": "C", "end": 6249, "referenceAllele": "T", "start": 6248 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544040.1:c.*37T>C" ], "proteinEffect": { "hgvs": "XP_011542342.1:n.*37T>C" }, "referenceSequence": "http://reg.genome.network/refseq/RS110953" }, { "coordinates": [ { "allele": "C", "end": 6490, "referenceAllele": "T", "start": 6489 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.2:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542335.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS555477" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544035.2:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542337.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542337.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS555478" }, { "coordinates": [ { "allele": "C", "end": 3994, "referenceAllele": "T", "start": 3993 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544036.2:c.3821T>C" ], "proteinEffect": { "hgvs": "XP_011542338.1:p.Met1274Thr", "hgvsWellDefined": "XP_011542338.1:p.Met1274Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS555479" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544037.2:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542339.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542339.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS555480" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544039.2:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_011542341.1:p.Met2053Thr", "hgvsWellDefined": "XP_011542341.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS555481" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_017000150.1:c.6158T>C" ], "proteinEffect": { "hgvs": "XP_016855639.1:p.Met2053Thr", "hgvsWellDefined": "XP_016855639.1:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS556567" }, { "coordinates": [ { "allele": "C", "end": 6111, "referenceAllele": "T", "start": 6110 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_017000151.1:c.*37T>C" ], "proteinEffect": { "hgvs": "XP_016855640.1:n.*37T>C" }, "referenceSequence": "http://reg.genome.network/refseq/RS556568" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736946.2:n.6340T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS587794" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736947.1:n.6340T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS587795" }, { "coordinates": [ { "allele": "C", "end": 6340, "referenceAllele": "T", "start": 6339 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736948.1:n.6340T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS587796" }, { "coordinates": [ { "allele": "C", "end": 6249, "referenceAllele": "T", "start": 6248 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_002959252.1:n.6249T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS605185" }, { "@id": "http://reg.genome.network/allele/PA2825049281", "coordinates": [ { "allele": "C", "end": 6319, "referenceAllele": "T", "start": 6318 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_000081.4:c.6158T>C" ], "proteinEffect": { "hgvs": "NP_000072.2:p.Met2053Thr", "hgvsWellDefined": "NP_000072.2:p.Met2053Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS674690", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.6158T>C" }, "RefSeq": { "hgvs": "NM_000081.4:c.6158T>C" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Met2053Thr" }, "RefSeq": { "hgvs": "NP_000072.2:p.Met2053Thr" } } } } ], "type": "nucleotide" }