{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA257003", "communityStandardTitle": [ "NM_000245.4(MET):c.3689A>G (p.Tyr1230Cys)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=699", "active": true, "id": "COSM699" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=28924[alleleid]", "alleleId": 28924, "preferredName": "NM_000245.4(MET):c.3689A>G (p.Tyr1230Cys)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/13885", "RCV": [ "RCV000014899", "RCV000441479", "RCV000430628", "RCV000420374", "RCV001851861", "RCV002362584" ], "variationId": 13885 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr7:g.116423414A>G?assembly=hg19", "id": "chr7:g.116423414A>G" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr7:g.116783360A>G?assembly=hg38", "id": "chr7:g.116783360A>G" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/121913246", "rs": 121913246 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/7-116423414-A-G?dataset=gnomad_r2_1", "id": "7-116423414-A-G", "variant": "7:116423414 A / G" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/7-116783360-A-G?dataset=gnomad_r4", "id": "7-116783360-A-G", "variant": "7:116783360 A / G" } ] }, "genomicAlleles": [ { "chromosome": "7", "coordinates": [ { "allele": "G", "end": 116783360, "referenceAllele": "A", "start": 116783359 } ], "hgvs": [ "NC_000007.14:g.116783360A>G", "CM000669.2:g.116783360A>G" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000055" }, { "chromosome": "7", "coordinates": [ { "allele": "G", "end": 116423414, "referenceAllele": "A", "start": 116423413 } ], "hgvs": [ "NC_000007.13:g.116423414A>G", "CM000669.1:g.116423414A>G" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000031" }, { "chromosome": "7", "coordinates": [ { "allele": "G", "end": 116210650, "referenceAllele": "A", "start": 116210649 } ], "hgvs": [ "NC_000007.12:g.116210650A>G" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000007" }, { "coordinates": [ { "allele": "G", "end": 115956, "referenceAllele": "A", "start": 115955 } ], "hgvs": [ "NG_008996.1:g.115956A>G", "LRG_662:g.115956A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS001367" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "G", "end": 3985, "referenceAllele": "A", "start": 3984 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "ENST00000436117.3:c.*1294A>G" ], "proteinEffect": { "hgvs": "ENSP00000410980.2:n.*1294A>G" }, "referenceSequence": "http://reg.genome.network/refseq/RS914063" }, { "coordinates": [ { "allele": "G", "end": 4139, "referenceAllele": "A", "start": 4138 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "ENST00000318493.11:c.3743A>G" ], "proteinEffect": { "hgvs": "ENSP00000317272.6:p.Tyr1248Cys", "hgvsWellDefined": "ENSP00000317272.6:p.Tyr1248Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS746223" }, { "coordinates": [ { "allele": "G", "end": 4085, "referenceAllele": "A", "start": 4084 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "ENST00000397752.8:c.3689A>G" ], "proteinEffect": { "hgvs": "ENSP00000380860.3:p.Tyr1230Cys", "hgvsWellDefined": "ENSP00000380860.3:p.Tyr1230Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS753679", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000397752.8:c.3689A>G" }, "RefSeq": { "hgvs": "NM_000245.4:c.3689A>G" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000380860.3:p.Tyr1230Cys" }, "RefSeq": { "hgvs": "NP_000236.2:p.Tyr1230Cys" } } } }, { "coordinates": [ { "allele": "G", "end": 3930, "referenceAllele": "A", "start": 3929 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "ENST00000318493.10:c.3743A>G" ], "proteinEffect": { "hgvs": "ENSP00000317272.6:p.Tyr1248Cys", "hgvsWellDefined": "ENSP00000317272.6:p.Tyr1248Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS257541" }, { "coordinates": [ { "allele": "G", "end": 3889, "referenceAllele": "A", "start": 3888 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "ENST00000397752.7:c.3689A>G" ], "proteinEffect": { "hgvs": "ENSP00000380860.3:p.Tyr1230Cys", "hgvsWellDefined": "ENSP00000380860.3:p.Tyr1230Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS277959" }, { "@id": "http://reg.genome.network/allele/PA093836", "coordinates": [ { "allele": "G", "end": 3876, "referenceAllele": "A", "start": 3875 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "NM_000245.2:c.3689A>G" ], "proteinEffect": { "hgvs": "NP_000236.2:p.Tyr1230Cys", "hgvsWellDefined": "NP_000236.2:p.Tyr1230Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS006307" }, { "@id": "http://reg.genome.network/allele/PA257005", "coordinates": [ { "allele": "G", "end": 3930, "referenceAllele": "A", "start": 3929 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "NM_001127500.1:c.3743A>G", "LRG_662t1:c.3743A>G" ], "proteinEffect": { "hgvs": "NP_001120972.1:p.Tyr1248Cys", "hgvsWellDefined": "NP_001120972.1:p.Tyr1248Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS011629" }, { "coordinates": [ { "allele": "G", "end": 2630, "referenceAllele": "A", "start": 2629 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "XM_006715990.2:c.2399A>G" ], "proteinEffect": { "hgvs": "XP_006716053.1:p.Tyr800Cys", "hgvsWellDefined": "XP_006716053.1:p.Tyr800Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS071450" }, { "coordinates": [ { "allele": "G", "end": 2612, "referenceAllele": "A", "start": 2611 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "XM_006715991.2:c.2399A>G" ], "proteinEffect": { "hgvs": "XP_006716054.1:p.Tyr800Cys", "hgvsWellDefined": "XP_006716054.1:p.Tyr800Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS071451" }, { "coordinates": [ { "allele": "G", "end": 3920, "referenceAllele": "A", "start": 3919 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "XM_011516223.1:c.3746A>G" ], "proteinEffect": { "hgvs": "XP_011514525.1:p.Tyr1249Cys", "hgvsWellDefined": "XP_011514525.1:p.Tyr1249Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS083426" }, { "@id": "http://reg.genome.network/allele/PA093836", "coordinates": [ { "allele": "G", "end": 3891, "referenceAllele": "A", "start": 3890 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "NM_000245.3:c.3689A>G" ], "proteinEffect": { "hgvs": "NP_000236.2:p.Tyr1230Cys", "hgvsWellDefined": "NP_000236.2:p.Tyr1230Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS510772" }, { "@id": "http://reg.genome.network/allele/PA257005", "coordinates": [ { "allele": "G", "end": 3945, "referenceAllele": "A", "start": 3944 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "NM_001127500.2:c.3743A>G" ], "proteinEffect": { "hgvs": "NP_001120972.1:p.Tyr1248Cys", "hgvsWellDefined": "NP_001120972.1:p.Tyr1248Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS511410" }, { "@id": "http://reg.genome.network/allele/PA916027578", "coordinates": [ { "allele": "G", "end": 2708, "referenceAllele": "A", "start": 2707 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "NM_001324402.1:c.2399A>G" ], "proteinEffect": { "hgvs": "NP_001311331.1:p.Tyr800Cys", "hgvsWellDefined": "NP_001311331.1:p.Tyr800Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS515982" }, { "coordinates": [ { "allele": "G", "end": 3820, "referenceAllele": "A", "start": 3819 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "XR_001744772.1:n.3820A>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS593445" }, { "@id": "http://reg.genome.network/allele/PA257005", "coordinates": [ { "allele": "G", "end": 4139, "referenceAllele": "A", "start": 4138 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "NM_001127500.3:c.3743A>G" ], "proteinEffect": { "hgvs": "NP_001120972.1:p.Tyr1248Cys", "hgvsWellDefined": "NP_001120972.1:p.Tyr1248Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS663551" }, { "@id": "http://reg.genome.network/allele/PA093836", "coordinates": [ { "allele": "G", "end": 4085, "referenceAllele": "A", "start": 4084 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "NM_000245.4:c.3689A>G" ], "proteinEffect": { "hgvs": "NP_000236.2:p.Tyr1230Cys", "hgvsWellDefined": "NP_000236.2:p.Tyr1230Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS674760", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000397752.8:c.3689A>G" }, "RefSeq": { "hgvs": "NM_000245.4:c.3689A>G" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000380860.3:p.Tyr1230Cys" }, "RefSeq": { "hgvs": "NP_000236.2:p.Tyr1230Cys" } } } }, { "@id": "http://reg.genome.network/allele/PA916027578", "coordinates": [ { "allele": "G", "end": 2871, "referenceAllele": "A", "start": 2870 } ], "gene": "http://reg.genome.network/gene/GN007029", "geneNCBI_id": 4233, "geneSymbol": "MET", "hgvs": [ "NM_001324402.2:c.2399A>G" ], "proteinEffect": { "hgvs": "NP_001311331.1:p.Tyr800Cys", "hgvsWellDefined": "NP_001311331.1:p.Tyr800Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS686384" } ], "type": "nucleotide" }