{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA347084", "communityStandardTitle": [ "NM_000081.4(LYST):c.772T>C (p.Cys258Arg)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=178796[alleleid]", "alleleId": 178796, "preferredName": "NM_000081.4(LYST):c.772T>C (p.Cys258Arg)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/180622", "RCV": [ "RCV000192043" ], "variationId": 180622 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235973346A>G?assembly=hg19", "id": "chr1:g.235973346A>G" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235810046A>G?assembly=hg38", "id": "chr1:g.235810046A>G" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/797044534", "rs": 797044534 } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-235810046-A-G?dataset=gnomad_r3", "id": "1-235810046-A-G", "variant": "1:235810046 A / G" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-235810046-A-G?dataset=gnomad_r4", "id": "1-235810046-A-G", "variant": "1:235810046 A / G" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "G", "end": 235810046, "referenceAllele": "A", "start": 235810045 } ], "hgvs": [ "NC_000001.11:g.235810046A>G", "CM000663.2:g.235810046A>G" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "G", "end": 235973346, "referenceAllele": "A", "start": 235973345 } ], "hgvs": [ "NC_000001.10:g.235973346A>G", "CM000663.1:g.235973346A>G" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "G", "end": 234039969, "referenceAllele": "A", "start": 234039968 } ], "hgvs": [ "NC_000001.9:g.234039969A>G" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "C", "end": 78595, "referenceAllele": "T", "start": 78594 } ], "hgvs": [ "NG_007397.1:g.78595T>C", "LRG_143:g.78595T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS000565" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "C", "end": 1255, "referenceAllele": "T", "start": 1254 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697178.1:c.772T>C" ], "proteinEffect": { "hgvs": "ENSP00000513163.1:p.Cys258Arg", "hgvsWellDefined": "ENSP00000513163.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS908583" }, { "coordinates": [ { "allele": "C", "end": 423, "endIntronDirection": "-", "endIntronOffset": 108, "referenceAllele": "T", "start": 423, "startIntronDirection": "-", "startIntronOffset": 109 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697242.1:c.284-109T>C" ], "proteinEffect": { "hgvs": "ENSP00000513207.1:n.284-109T>C" }, "referenceSequence": "http://reg.genome.network/refseq/RS908630" }, { "coordinates": [ { "allele": "C", "end": 933, "referenceAllele": "T", "start": 932 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.7:c.772T>C" ], "proteinEffect": { "hgvs": "ENSP00000374443.2:p.Cys258Arg", "hgvsWellDefined": "ENSP00000374443.2:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS752840", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.772T>C" }, "RefSeq": { "hgvs": "NM_000081.4:c.772T>C" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Cys258Arg" }, "RefSeq": { "hgvs": "NP_000072.2:p.Cys258Arg" } } } }, { "coordinates": [ { "allele": "C", "end": 947, "referenceAllele": "T", "start": 946 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.6:c.772T>C" ], "proteinEffect": { "hgvs": "ENSP00000374443.2:p.Cys258Arg", "hgvsWellDefined": "ENSP00000374443.2:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS274290" }, { "coordinates": [ { "allele": "C", "end": 951, "referenceAllele": "T", "start": 950 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389794.7:c.772T>C" ], "proteinEffect": { "hgvs": "ENSP00000374444.4:p.Cys258Arg", "hgvsWellDefined": "ENSP00000374444.4:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS274291" }, { "coordinates": [ { "allele": "C", "end": 1323, "referenceAllele": "T", "start": 1322 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000465349.5:n.1323T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS308972" }, { "coordinates": [ { "allele": "C", "end": 1323, "referenceAllele": "T", "start": 1322 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000489585.5:n.1323T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS327618" }, { "@id": "http://reg.genome.network/allele/PA347087", "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_000081.3:c.772T>C", "LRG_143t1:c.772T>C" ], "proteinEffect": { "hgvs": "NP_000072.2:p.Cys258Arg", "hgvsWellDefined": "NP_000072.2:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS006145" }, { "@id": "http://reg.genome.network/allele/PA347088", "coordinates": [ { "allele": "C", "end": 1391, "referenceAllele": "T", "start": 1390 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_001301365.1:c.772T>C", "LRG_143t2:c.772T>C" ], "proteinEffect": { "hgvs": "NP_001288294.1:p.Cys258Arg", "hgvsWellDefined": "NP_001288294.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS025192" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544031.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542333.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542333.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS110944" }, { "coordinates": [ { "allele": "C", "end": 1357, "referenceAllele": "T", "start": 1356 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544032.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542334.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542334.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS110945" }, { "coordinates": [ { "allele": "C", "end": 1155, "referenceAllele": "T", "start": 1154 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542335.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS110946" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544034.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542336.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542336.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS110947" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544035.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542337.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542337.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS110948" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544037.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542339.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542339.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS110950" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544038.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542340.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542340.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS110951" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544039.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542341.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542341.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS110952" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544040.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542342.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542342.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS110953" }, { "coordinates": [ { "allele": "C", "end": 1104, "referenceAllele": "T", "start": 1103 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.2:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542335.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS555477" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544035.2:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542337.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542337.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS555478" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544037.2:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542339.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542339.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS555480" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544039.2:c.772T>C" ], "proteinEffect": { "hgvs": "XP_011542341.1:p.Cys258Arg", "hgvsWellDefined": "XP_011542341.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS555481" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_017000150.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_016855639.1:p.Cys258Arg", "hgvsWellDefined": "XP_016855639.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS556567" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_017000151.1:c.772T>C" ], "proteinEffect": { "hgvs": "XP_016855640.1:p.Cys258Arg", "hgvsWellDefined": "XP_016855640.1:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS556568" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736946.2:n.954T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS587794" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736947.1:n.954T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS587795" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736948.1:n.954T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS587796" }, { "coordinates": [ { "allele": "C", "end": 954, "referenceAllele": "T", "start": 953 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_002959252.1:n.954T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS605185" }, { "@id": "http://reg.genome.network/allele/PA347087", "coordinates": [ { "allele": "C", "end": 933, "referenceAllele": "T", "start": 932 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_000081.4:c.772T>C" ], "proteinEffect": { "hgvs": "NP_000072.2:p.Cys258Arg", "hgvsWellDefined": "NP_000072.2:p.Cys258Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS674690", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.772T>C" }, "RefSeq": { "hgvs": "NM_000081.4:c.772T>C" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Cys258Arg" }, "RefSeq": { "hgvs": "NP_000072.2:p.Cys258Arg" } } } } ], "type": "nucleotide" }