{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA008005", "communityStandardTitle": [ "NM_020975.6(RET):c.1853G>A (p.Cys618Tyr)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=980", "active": true, "id": "COSM980" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=5610490", "active": true, "id": "COSM5610490" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=36242[alleleid]", "alleleId": 36242, "preferredName": "NM_020975.6(RET):c.1853G>A (p.Cys618Tyr)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/24901", "RCV": [ "RCV000163667", "RCV000429944", "RCV000423173", "RCV000434317", "RCV000440162", "RCV000475953", "RCV000424049", "RCV001565486" ], "variationId": 24901 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.43609097G>A?assembly=hg19", "id": "chr10:g.43609097G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.43113649G>A?assembly=hg38", "id": "chr10:g.43113649G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/79781594", "rs": 79781594 } ] }, "genomicAlleles": [ { "chromosome": "10", "coordinates": [ { "allele": "A", "end": 43113649, "referenceAllele": "G", "start": 43113648 } ], "hgvs": [ "NC_000010.11:g.43113649G>A", "CM000672.2:g.43113649G>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000058" }, { "chromosome": "10", "coordinates": [ { "allele": "A", "end": 43609097, "referenceAllele": "G", "start": 43609096 } ], "hgvs": [ "NC_000010.10:g.43609097G>A", "CM000672.1:g.43609097G>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000034" }, { "chromosome": "10", "coordinates": [ { "allele": "A", "end": 42929103, "referenceAllele": "G", "start": 42929102 } ], "hgvs": [ "NC_000010.9:g.42929103G>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000010" }, { "coordinates": [ { "allele": "A", "end": 41581, "referenceAllele": "G", "start": 41580 } ], "hgvs": [ "NG_007489.1:g.41581G>A", "LRG_518:g.41581G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000611" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1630, "referenceAllele": "G", "start": 1629 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000615310.5:c.1457G>A" ], "proteinEffect": { "hgvs": "ENSP00000480088.2:p.Cys486Tyr", "hgvsWellDefined": "ENSP00000480088.2:p.Cys486Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS826472" }, { "coordinates": [ { "allele": "A", "end": 1427, "referenceAllele": "G", "start": 1426 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000683007.1:n.1427G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS827994" }, { "coordinates": [ { "allele": "A", "end": 614, "referenceAllele": "G", "start": 613 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000683872.1:n.614G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS828839" }, { "coordinates": [ { "allele": "A", "end": 2043, "referenceAllele": "G", "start": 2042 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000340058.6:c.1853G>A" ], "proteinEffect": { "hgvs": "ENSP00000344798.4:p.Cys618Tyr", "hgvsWellDefined": "ENSP00000344798.4:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS747868" }, { "coordinates": [ { "allele": "A", "end": 2043, "referenceAllele": "G", "start": 2042 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000355710.8:c.1853G>A" ], "proteinEffect": { "hgvs": "ENSP00000347942.3:p.Cys618Tyr", "hgvsWellDefined": "ENSP00000347942.3:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS748710", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000355710.8:c.1853G>A" }, "RefSeq": { "hgvs": "NM_020975.6:c.1853G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000347942.3:p.Cys618Tyr" }, "RefSeq": { "hgvs": "NP_066124.1:p.Cys618Tyr" } } } }, { "coordinates": [ { "allele": "A", "end": 1410, "referenceAllele": "G", "start": 1409 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000671844.1:c.*447G>A" ], "proteinEffect": { "hgvs": "ENSP00000500541.1:n.*447G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS773184" }, { "coordinates": [ { "allele": "A", "end": 853, "referenceAllele": "G", "start": 852 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000672389.1:c.*447G>A" ], "proteinEffect": { "hgvs": "ENSP00000500252.1:n.*447G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS773367" }, { "coordinates": [ { "allele": "A", "end": 2033, "referenceAllele": "G", "start": 2032 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000340058.5:c.1853G>A" ], "proteinEffect": { "hgvs": "ENSP00000344798.4:p.Cys618Tyr", "hgvsWellDefined": "ENSP00000344798.4:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS247408" }, { "coordinates": [ { "allele": "A", "end": 2085, "referenceAllele": "G", "start": 2084 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000355710.7:c.1853G>A" ], "proteinEffect": { "hgvs": "ENSP00000347942.3:p.Cys618Tyr", "hgvsWellDefined": "ENSP00000347942.3:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS247251" }, { "coordinates": [ { "allele": "A", "end": 589, "referenceAllele": "G", "start": 588 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000498820.5:c.404G>A" ], "proteinEffect": { "hgvs": "ENSP00000419080.1:p.Cys135Tyr", "hgvsWellDefined": "ENSP00000419080.1:p.Cys135Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS247185" }, { "coordinates": [ { "allele": "A", "end": 1479, "endIntronDirection": "+", "endIntronOffset": 2417, "referenceAllele": "G", "start": 1479, "startIntronDirection": "+", "startIntronOffset": 2416 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "ENST00000615310.4:c.1289+2417G>A" ], "proteinEffect": { "hgvs": "ENSP00000480088.1:n.1289+2417G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS402558" }, { "@id": "http://reg.genome.network/allele/PA128193", "coordinates": [ { "allele": "A", "end": 2043, "referenceAllele": "G", "start": 2042 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020630.4:c.1853G>A", "LRG_518t2:c.1853G>A" ], "proteinEffect": { "hgvs": "NP_065681.1:p.Cys618Tyr", "hgvsWellDefined": "NP_065681.1:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS036456" }, { "@id": "http://reg.genome.network/allele/PA106722", "coordinates": [ { "allele": "A", "end": 2043, "referenceAllele": "G", "start": 2042 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020975.4:c.1853G>A", "LRG_518t1:c.1853G>A" ], "proteinEffect": { "hgvs": "NP_066124.1:p.Cys618Tyr", "hgvsWellDefined": "NP_066124.1:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS036733" }, { "coordinates": [ { "allele": "A", "end": 2085, "referenceAllele": "G", "start": 2084 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "XM_011540027.1:c.1853G>A" ], "proteinEffect": { "hgvs": "XP_011538329.1:p.Cys618Tyr", "hgvsWellDefined": "XP_011538329.1:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS106977" }, { "@id": "http://reg.genome.network/allele/PA2828047521", "coordinates": [ { "allele": "A", "end": 1448, "referenceAllele": "G", "start": 1447 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_001355216.1:c.1091G>A" ], "proteinEffect": { "hgvs": "NP_001342145.1:p.Cys364Tyr", "hgvsWellDefined": "NP_001342145.1:p.Cys364Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS522845" }, { "@id": "http://reg.genome.network/allele/PA128193", "coordinates": [ { "allele": "A", "end": 2085, "referenceAllele": "G", "start": 2084 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020630.5:c.1853G>A" ], "proteinEffect": { "hgvs": "NP_065681.1:p.Cys618Tyr", "hgvsWellDefined": "NP_065681.1:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS525983" }, { "@id": "http://reg.genome.network/allele/PA106722", "coordinates": [ { "allele": "A", "end": 2085, "referenceAllele": "G", "start": 2084 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020975.5:c.1853G>A" ], "proteinEffect": { "hgvs": "NP_066124.1:p.Cys618Tyr", "hgvsWellDefined": "NP_066124.1:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS526025" }, { "@id": "http://reg.genome.network/allele/PA106722", "coordinates": [ { "allele": "A", "end": 2043, "referenceAllele": "G", "start": 2042 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020975.6:c.1853G>A" ], "proteinEffect": { "hgvs": "NP_066124.1:p.Cys618Tyr", "hgvsWellDefined": "NP_066124.1:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS670171", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000355710.8:c.1853G>A" }, "RefSeq": { "hgvs": "NM_020975.6:c.1853G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000347942.3:p.Cys618Tyr" }, "RefSeq": { "hgvs": "NP_066124.1:p.Cys618Tyr" } } } }, { "@id": "http://reg.genome.network/allele/PA128193", "coordinates": [ { "allele": "A", "end": 2043, "referenceAllele": "G", "start": 2042 } ], "gene": "http://reg.genome.network/gene/GN009967", "geneNCBI_id": 5979, "geneSymbol": "RET", "hgvs": [ "NM_020630.6:c.1853G>A" ], "proteinEffect": { "hgvs": "NP_065681.1:p.Cys618Tyr", "hgvsWellDefined": "NP_065681.1:p.Cys618Tyr" }, "referenceSequence": "http://reg.genome.network/refseq/RS728447" } ], "type": "nucleotide" }