{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA349077944", "communityStandardTitle": [ "NM_001365536.1(SCN9A):c.2620G>A (p.Ala874Thr)" ], "externalRecords": { "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.167133747C>T?assembly=hg19", "id": "chr2:g.167133747C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.166277237C>T?assembly=hg38", "id": "chr2:g.166277237C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/80356477", "rs": 80356477 } ] }, "genomicAlleles": [ { "chromosome": "2", "coordinates": [ { "allele": "T", "end": 166277237, "referenceAllele": "C", "start": 166277236 } ], "hgvs": [ "NC_000002.12:g.166277237C>T", "CM000664.2:g.166277237C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000050" }, { "chromosome": "2", "coordinates": [ { "allele": "T", "end": 167133747, "referenceAllele": "C", "start": 167133746 } ], "hgvs": [ "NC_000002.11:g.167133747C>T", "CM000664.1:g.167133747C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000026" }, { "chromosome": "2", "coordinates": [ { "allele": "T", "end": 166841993, "referenceAllele": "C", "start": 166841992 } ], "hgvs": [ "NC_000002.10:g.166841993C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000002" }, { "coordinates": [ { "allele": "A", "end": 103751, "referenceAllele": "G", "start": 103750 } ], "hgvs": [ "NG_012798.1:g.103751G>A", "LRG_369:g.103751G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS002537" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 2868, "referenceAllele": "G", "start": 2867 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000303354.11:c.2620G>A" ], "proteinEffect": { "hgvs": "ENSP00000304748.7:p.Ala874Thr", "hgvsWellDefined": "ENSP00000304748.7:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS745024" }, { "coordinates": [ { "allele": "A", "end": 2620, "referenceAllele": "G", "start": 2619 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000409435.6:c.2620G>A" ], "proteinEffect": { "hgvs": "ENSP00000386330.2:p.Ala874Thr", "hgvsWellDefined": "ENSP00000386330.2:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS754301" }, { "coordinates": [ { "allele": "A", "end": 2918, "referenceAllele": "G", "start": 2917 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000642356.2:c.2620G>A" ], "proteinEffect": { "hgvs": "ENSP00000495601.1:p.Ala874Thr", "hgvsWellDefined": "ENSP00000495601.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS766697", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000642356.2:c.2620G>A" }, "RefSeq": { "hgvs": "NM_001365536.1:c.2620G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000495601.1:p.Ala874Thr" }, "RefSeq": { "hgvs": "NP_001352465.1:p.Ala874Thr" } } } }, { "coordinates": [ { "allele": "A", "end": 2587, "referenceAllele": "G", "start": 2586 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000644316.1:c.2587G>A" ], "proteinEffect": { "hgvs": "ENSP00000493939.1:p.Ala863Thr", "hgvsWellDefined": "ENSP00000493939.1:p.Ala863Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS767756" }, { "coordinates": [ { "allele": "A", "end": 277, "referenceAllele": "G", "start": 276 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000645283.1:c.277G>A" ], "proteinEffect": { "hgvs": "ENSP00000496086.1:p.Ala93Thr", "hgvsWellDefined": "ENSP00000496086.1:p.Ala93Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS768267" }, { "coordinates": [ { "allele": "A", "end": 2835, "referenceAllele": "G", "start": 2834 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000645907.1:c.2587G>A" ], "proteinEffect": { "hgvs": "ENSP00000495983.1:p.Ala863Thr", "hgvsWellDefined": "ENSP00000495983.1:p.Ala863Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS768602" }, { "coordinates": [ { "allele": "A", "end": 1622, "referenceAllele": "G", "start": 1621 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000667201.2:c.1622G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS772970" }, { "coordinates": [ { "allele": "A", "end": 2961, "referenceAllele": "G", "start": 2960 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000303354.10:c.2620G>A" ], "proteinEffect": { "hgvs": "ENSP00000304748.7:p.Ala874Thr", "hgvsWellDefined": "ENSP00000304748.7:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS255307" }, { "coordinates": [ { "allele": "A", "end": 2620, "referenceAllele": "G", "start": 2619 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000409435.5:c.2620G>A" ], "proteinEffect": { "hgvs": "ENSP00000386330.1:p.Ala874Thr", "hgvsWellDefined": "ENSP00000386330.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS281545" }, { "coordinates": [ { "allele": "A", "end": 2934, "referenceAllele": "G", "start": 2933 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "ENST00000409672.5:c.2587G>A" ], "proteinEffect": { "hgvs": "ENSP00000386306.1:p.Ala863Thr", "hgvsWellDefined": "ENSP00000386306.1:p.Ala863Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS281751" }, { "@id": "http://reg.genome.network/allele/PA3066520310", "coordinates": [ { "allele": "A", "end": 2928, "referenceAllele": "G", "start": 2927 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "NM_002977.3:c.2587G>A", "LRG_369t1:c.2587G>A" ], "proteinEffect": { "hgvs": "NP_002968.1:p.Ala863Thr", "hgvsWellDefined": "NP_002968.1:p.Ala863Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS028260" }, { "coordinates": [ { "allele": "T", "end": 1019, "referenceAllele": "C", "start": 1018 } ], "gene": "http://reg.genome.network/gene/GN054069", "geneNCBI_id": 101929680, "geneSymbol": "SCN1A-AS1", "hgvs": [ "NR_110260.1:n.1019C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS054541" }, { "coordinates": [ { "allele": "A", "end": 2934, "referenceAllele": "G", "start": 2933 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_005246757.1:c.2620G>A" ], "proteinEffect": { "hgvs": "XP_005246814.1:p.Ala874Thr", "hgvsWellDefined": "XP_005246814.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS057779" }, { "coordinates": [ { "allele": "A", "end": 2882, "referenceAllele": "G", "start": 2881 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_011511616.1:c.2620G>A" ], "proteinEffect": { "hgvs": "XP_011509918.1:p.Ala874Thr", "hgvsWellDefined": "XP_011509918.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS078877" }, { "coordinates": [ { "allele": "A", "end": 2934, "referenceAllele": "G", "start": 2933 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_011511617.1:c.2620G>A" ], "proteinEffect": { "hgvs": "XP_011509919.1:p.Ala874Thr", "hgvsWellDefined": "XP_011509919.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS078878" }, { "coordinates": [ { "allele": "A", "end": 2901, "referenceAllele": "G", "start": 2900 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_011511618.1:c.2587G>A" ], "proteinEffect": { "hgvs": "XP_011509920.1:p.Ala863Thr", "hgvsWellDefined": "XP_011509920.1:p.Ala863Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS078879" }, { "coordinates": [ { "allele": "A", "end": 2934, "referenceAllele": "G", "start": 2933 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_011511619.1:c.2620G>A" ], "proteinEffect": { "hgvs": "XP_011509921.1:p.Ala874Thr", "hgvsWellDefined": "XP_011509921.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS078880" }, { "coordinates": [ { "allele": "A", "end": 2918, "referenceAllele": "G", "start": 2917 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "NM_001365536.1:c.2620G>A" ], "proteinEffect": { "hgvs": "NP_001352465.1:p.Ala874Thr", "hgvsWellDefined": "NP_001352465.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS524144", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000642356.2:c.2620G>A" }, "RefSeq": { "hgvs": "NM_001365536.1:c.2620G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000495601.1:p.Ala874Thr" }, "RefSeq": { "hgvs": "NP_001352465.1:p.Ala874Thr" } } } }, { "coordinates": [ { "allele": "A", "end": 2896, "referenceAllele": "G", "start": 2895 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_011511616.3:c.2620G>A" ], "proteinEffect": { "hgvs": "XP_011509918.1:p.Ala874Thr", "hgvsWellDefined": "XP_011509918.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS542212" }, { "coordinates": [ { "allele": "A", "end": 2934, "referenceAllele": "G", "start": 2933 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_011511617.2:c.2620G>A" ], "proteinEffect": { "hgvs": "XP_011509919.1:p.Ala874Thr", "hgvsWellDefined": "XP_011509919.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS542213" }, { "coordinates": [ { "allele": "A", "end": 2901, "referenceAllele": "G", "start": 2900 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_011511618.2:c.2587G>A" ], "proteinEffect": { "hgvs": "XP_011509920.1:p.Ala863Thr", "hgvsWellDefined": "XP_011509920.1:p.Ala863Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS542214" }, { "coordinates": [ { "allele": "A", "end": 2934, "referenceAllele": "G", "start": 2933 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_011511619.2:c.2620G>A" ], "proteinEffect": { "hgvs": "XP_011509921.1:p.Ala874Thr", "hgvsWellDefined": "XP_011509921.1:p.Ala874Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS542215" }, { "coordinates": [ { "allele": "A", "end": 2463, "referenceAllele": "G", "start": 2462 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_017004668.1:c.2233G>A" ], "proteinEffect": { "hgvs": "XP_016860157.1:p.Ala745Thr", "hgvsWellDefined": "XP_016860157.1:p.Ala745Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS560118" }, { "coordinates": [ { "allele": "A", "end": 2021, "referenceAllele": "G", "start": 2020 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XM_017004669.1:c.1876G>A" ], "proteinEffect": { "hgvs": "XP_016860158.1:p.Ala626Thr", "hgvsWellDefined": "XP_016860158.1:p.Ala626Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS560119" }, { "coordinates": [ { "allele": "A", "end": 2934, "referenceAllele": "G", "start": 2933 } ], "gene": "http://reg.genome.network/gene/GN010597", "geneNCBI_id": 6335, "geneSymbol": "SCN9A", "hgvs": [ "XR_001738886.1:n.2934G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS589322" } ], "type": "nucleotide" }