{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA5297847", "communityStandardTitle": [ "NM_015046.7(SETX):c.1066G>A (p.Val356Ile)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=1460702", "active": true, "id": "COSM1460702" }, { "active": false, "id": "COSM4785326" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=835626[alleleid]", "alleleId": 835626, "preferredName": "NM_015046.7(SETX):c.1066G>A (p.Val356Ile)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/845589", "RCV": [ "RCV001048687", "RCV001508272", "RCV002409420", "RCV003233938", "RCV003233939" ], "variationId": 845589 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/9-135206471-C-T", "id": "9-135206471-C-T", "variant": "9:135206471 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr9:g.135206471C>T?assembly=hg19", "id": "chr9:g.135206471C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr9:g.132331084C>T?assembly=hg38", "id": "chr9:g.132331084C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/143270460", "rs": 143270460 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/9-135206471-C-T?dataset=gnomad_r2_1", "id": "9-135206471-C-T", "variant": "9:135206471 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/9-132331084-C-T?dataset=gnomad_r3", "id": "9-132331084-C-T", "variant": "9:132331084 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/9-132331084-C-T?dataset=gnomad_r4", "id": "9-132331084-C-T", "variant": "9:132331084 C / T" } ] }, "genomicAlleles": [ { "chromosome": "9", "coordinates": [ { "allele": "T", "end": 132331084, "referenceAllele": "C", "start": 132331083 } ], "hgvs": [ "NC_000009.12:g.132331084C>T", "CM000671.2:g.132331084C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000057" }, { "chromosome": "9", "coordinates": [ { "allele": "T", "end": 135206471, "referenceAllele": "C", "start": 135206470 } ], "hgvs": [ "NC_000009.11:g.135206471C>T", "CM000671.1:g.135206471C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000033" }, { "chromosome": "9", "coordinates": [ { "allele": "T", "end": 134196292, "referenceAllele": "C", "start": 134196291 } ], "hgvs": [ "NC_000009.10:g.134196292C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000009" }, { "coordinates": [ { "allele": "A", "end": 28902, "referenceAllele": "G", "start": 28901 } ], "hgvs": [ "NG_007946.1:g.28902G>A", "LRG_268:g.28902G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000714" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "ENST00000224140.6:c.1066G>A" ], "proteinEffect": { "hgvs": "ENSP00000224140.5:p.Val356Ile", "hgvsWellDefined": "ENSP00000224140.5:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS740633", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000224140.6:c.1066G>A" }, "RefSeq": { "hgvs": "NM_015046.7:c.1066G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000224140.5:p.Val356Ile" }, "RefSeq": { "hgvs": "NP_055861.3:p.Val356Ile" } } } }, { "coordinates": [ { "allele": "A", "end": 1249, "referenceAllele": "G", "start": 1248 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "ENST00000224140.5:c.1066G>A" ], "proteinEffect": { "hgvs": "ENSP00000224140.5:p.Val356Ile", "hgvsWellDefined": "ENSP00000224140.5:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS248465" }, { "@id": "http://reg.genome.network/allele/PA1139727695", "coordinates": [ { "allele": "A", "end": 1249, "referenceAllele": "G", "start": 1248 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_015046.5:c.1066G>A", "LRG_268t1:c.1066G>A" ], "proteinEffect": { "hgvs": "NP_055861.3:p.Val356Ile", "hgvsWellDefined": "NP_055861.3:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS033695" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272171.1:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_005272228.1:p.Val356Ile", "hgvsWellDefined": "XP_005272228.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS067165" }, { "coordinates": [ { "allele": "A", "end": 1348, "referenceAllele": "G", "start": 1347 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272172.1:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_005272229.1:p.Val356Ile", "hgvsWellDefined": "XP_005272229.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS067166" }, { "coordinates": [ { "allele": "A", "end": 1386, "referenceAllele": "G", "start": 1385 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272173.1:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_005272230.1:p.Val356Ile", "hgvsWellDefined": "XP_005272230.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS067167" }, { "coordinates": [ { "allele": "A", "end": 1390, "referenceAllele": "G", "start": 1389 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518404.1:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_011516706.1:p.Val356Ile", "hgvsWellDefined": "XP_011516706.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS085578" }, { "coordinates": [ { "allele": "A", "end": 1204, "referenceAllele": "G", "start": 1203 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518405.1:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_011516707.1:p.Val356Ile", "hgvsWellDefined": "XP_011516707.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS085579" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518406.1:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_011516708.1:p.Val356Ile", "hgvsWellDefined": "XP_011516708.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS085580" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518407.1:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_011516709.1:p.Val356Ile", "hgvsWellDefined": "XP_011516709.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS085581" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518408.1:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_011516710.1:p.Val356Ile", "hgvsWellDefined": "XP_011516710.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS085582" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XR_929739.1:n.1250G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS125868" }, { "@id": "http://reg.genome.network/allele/PA2827616162", "coordinates": [ { "allele": "A", "end": 1386, "referenceAllele": "G", "start": 1385 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_001351527.1:c.1066G>A" ], "proteinEffect": { "hgvs": "NP_001338456.1:p.Val356Ile", "hgvsWellDefined": "NP_001338456.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS520290" }, { "@id": "http://reg.genome.network/allele/PA2827617491", "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_001351528.1:c.1066G>A" ], "proteinEffect": { "hgvs": "NP_001338457.1:p.Val356Ile", "hgvsWellDefined": "NP_001338457.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS520291" }, { "@id": "http://reg.genome.network/allele/PA1139727695", "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_015046.6:c.1066G>A" ], "proteinEffect": { "hgvs": "NP_055861.3:p.Val356Ile", "hgvsWellDefined": "NP_055861.3:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS525651" }, { "coordinates": [ { "allele": "A", "end": 1348, "referenceAllele": "G", "start": 1347 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272172.3:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_005272229.1:p.Val356Ile", "hgvsWellDefined": "XP_005272229.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS537256" }, { "coordinates": [ { "allele": "A", "end": 1386, "referenceAllele": "G", "start": 1385 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272173.3:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_005272230.1:p.Val356Ile", "hgvsWellDefined": "XP_005272230.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS537257" }, { "coordinates": [ { "allele": "A", "end": 1390, "referenceAllele": "G", "start": 1389 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518404.3:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_011516706.1:p.Val356Ile", "hgvsWellDefined": "XP_011516706.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS544905" }, { "coordinates": [ { "allele": "A", "end": 1408, "referenceAllele": "G", "start": 1407 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518405.3:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_011516707.1:p.Val356Ile", "hgvsWellDefined": "XP_011516707.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS544906" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518406.2:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_011516708.1:p.Val356Ile", "hgvsWellDefined": "XP_011516708.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS544907" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518408.3:c.1066G>A" ], "proteinEffect": { "hgvs": "XP_011516710.1:p.Val356Ile", "hgvsWellDefined": "XP_011516710.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS544908" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XR_001746251.1:n.1250G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS594602" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XR_929739.2:n.1250G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS609274" }, { "@id": "http://reg.genome.network/allele/PA1139727695", "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_015046.7:c.1066G>A" ], "proteinEffect": { "hgvs": "NP_055861.3:p.Val356Ile", "hgvsWellDefined": "NP_055861.3:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS668612", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000224140.6:c.1066G>A" }, "RefSeq": { "hgvs": "NM_015046.7:c.1066G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000224140.5:p.Val356Ile" }, "RefSeq": { "hgvs": "NP_055861.3:p.Val356Ile" } } } }, { "@id": "http://reg.genome.network/allele/PA2827617491", "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "G", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_001351528.2:c.1066G>A" ], "proteinEffect": { "hgvs": "NP_001338457.1:p.Val356Ile", "hgvsWellDefined": "NP_001338457.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS688870" }, { "@id": "http://reg.genome.network/allele/PA2827616162", "coordinates": [ { "allele": "A", "end": 1386, "referenceAllele": "G", "start": 1385 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_001351527.2:c.1066G>A" ], "proteinEffect": { "hgvs": "NP_001338456.1:p.Val356Ile", "hgvsWellDefined": "NP_001338456.1:p.Val356Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS719848" } ], "type": "nucleotide" }