{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA5297445", "communityStandardTitle": [ "NM_015046.7(SETX):c.3229G>A (p.Asp1077Asn)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=3699492", "active": true, "id": "COSM3699492" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=3699493", "active": true, "id": "COSM3699493" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=411571[alleleid]", "alleleId": 411571, "preferredName": "NM_015046.7(SETX):c.3229G>A (p.Asp1077Asn)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/424687", "RCV": [ "RCV000515959", "RCV000517650", "RCV001082564", "RCV001167391", "RCV001168005", "RCV001283502", "RCV002446949", "RCV003105922", "RCV004535538" ], "variationId": 424687 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/9-135203756-C-T", "id": "9-135203756-C-T", "variant": "9:135203756 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr9:g.135203756C>T?assembly=hg19", "id": "chr9:g.135203756C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr9:g.132328369C>T?assembly=hg38", "id": "chr9:g.132328369C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/145097270", "rs": 145097270 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/9-135203756-C-T?dataset=gnomad_r2_1", "id": "9-135203756-C-T", "variant": "9:135203756 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/9-132328369-C-T?dataset=gnomad_r3", "id": "9-132328369-C-T", "variant": "9:132328369 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/9-132328369-C-T?dataset=gnomad_r4", "id": "9-132328369-C-T", "variant": "9:132328369 C / T" } ] }, "genomicAlleles": [ { "chromosome": "9", "coordinates": [ { "allele": "T", "end": 132328369, "referenceAllele": "C", "start": 132328368 } ], "hgvs": [ "NC_000009.12:g.132328369C>T", "CM000671.2:g.132328369C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000057" }, { "chromosome": "9", "coordinates": [ { "allele": "T", "end": 135203756, "referenceAllele": "C", "start": 135203755 } ], "hgvs": [ "NC_000009.11:g.135203756C>T", "CM000671.1:g.135203756C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000033" }, { "chromosome": "9", "coordinates": [ { "allele": "T", "end": 134193577, "referenceAllele": "C", "start": 134193576 } ], "hgvs": [ "NC_000009.10:g.134193577C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000009" }, { "coordinates": [ { "allele": "A", "end": 31617, "referenceAllele": "G", "start": 31616 } ], "hgvs": [ "NG_007946.1:g.31617G>A", "LRG_268:g.31617G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000714" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "ENST00000224140.6:c.3229G>A" ], "proteinEffect": { "hgvs": "ENSP00000224140.5:p.Asp1077Asn", "hgvsWellDefined": "ENSP00000224140.5:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS740633", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000224140.6:c.3229G>A" }, "RefSeq": { "hgvs": "NM_015046.7:c.3229G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000224140.5:p.Asp1077Asn" }, "RefSeq": { "hgvs": "NP_055861.3:p.Asp1077Asn" } } } }, { "coordinates": [ { "allele": "A", "end": 3412, "referenceAllele": "G", "start": 3411 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "ENST00000224140.5:c.3229G>A" ], "proteinEffect": { "hgvs": "ENSP00000224140.5:p.Asp1077Asn", "hgvsWellDefined": "ENSP00000224140.5:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS248465" }, { "@id": "http://reg.genome.network/allele/PA658662228", "coordinates": [ { "allele": "A", "end": 3412, "referenceAllele": "G", "start": 3411 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_015046.5:c.3229G>A", "LRG_268t1:c.3229G>A" ], "proteinEffect": { "hgvs": "NP_055861.3:p.Asp1077Asn", "hgvsWellDefined": "NP_055861.3:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS033695" }, { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272171.1:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_005272228.1:p.Asp1077Asn", "hgvsWellDefined": "XP_005272228.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS067165" }, { "coordinates": [ { "allele": "A", "end": 3511, "referenceAllele": "G", "start": 3510 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272172.1:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_005272229.1:p.Asp1077Asn", "hgvsWellDefined": "XP_005272229.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS067166" }, { "coordinates": [ { "allele": "A", "end": 3549, "referenceAllele": "G", "start": 3548 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272173.1:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_005272230.1:p.Asp1077Asn", "hgvsWellDefined": "XP_005272230.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS067167" }, { "coordinates": [ { "allele": "A", "end": 3553, "referenceAllele": "G", "start": 3552 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518404.1:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_011516706.1:p.Asp1077Asn", "hgvsWellDefined": "XP_011516706.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS085578" }, { "coordinates": [ { "allele": "A", "end": 3367, "referenceAllele": "G", "start": 3366 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518405.1:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_011516707.1:p.Asp1077Asn", "hgvsWellDefined": "XP_011516707.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS085579" }, { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518406.1:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_011516708.1:p.Asp1077Asn", "hgvsWellDefined": "XP_011516708.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS085580" }, { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518407.1:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_011516709.1:p.Asp1077Asn", "hgvsWellDefined": "XP_011516709.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS085581" }, { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518408.1:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_011516710.1:p.Asp1077Asn", "hgvsWellDefined": "XP_011516710.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS085582" }, { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XR_929739.1:n.3413G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS125868" }, { "@id": "http://reg.genome.network/allele/PA2827616512", "coordinates": [ { "allele": "A", "end": 3549, "referenceAllele": "G", "start": 3548 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_001351527.1:c.3229G>A" ], "proteinEffect": { "hgvs": "NP_001338456.1:p.Asp1077Asn", "hgvsWellDefined": "NP_001338456.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS520290" }, { "@id": "http://reg.genome.network/allele/PA2827617841", "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_001351528.1:c.3229G>A" ], "proteinEffect": { "hgvs": "NP_001338457.1:p.Asp1077Asn", "hgvsWellDefined": "NP_001338457.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS520291" }, { "@id": "http://reg.genome.network/allele/PA658662228", "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_015046.6:c.3229G>A" ], "proteinEffect": { "hgvs": "NP_055861.3:p.Asp1077Asn", "hgvsWellDefined": "NP_055861.3:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS525651" }, { "coordinates": [ { "allele": "A", "end": 3511, "referenceAllele": "G", "start": 3510 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272172.3:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_005272229.1:p.Asp1077Asn", "hgvsWellDefined": "XP_005272229.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS537256" }, { "coordinates": [ { "allele": "A", "end": 3549, "referenceAllele": "G", "start": 3548 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_005272173.3:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_005272230.1:p.Asp1077Asn", "hgvsWellDefined": "XP_005272230.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS537257" }, { "coordinates": [ { "allele": "A", "end": 3553, "referenceAllele": "G", "start": 3552 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518404.3:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_011516706.1:p.Asp1077Asn", "hgvsWellDefined": "XP_011516706.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS544905" }, { "coordinates": [ { "allele": "A", "end": 3571, "referenceAllele": "G", "start": 3570 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518405.3:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_011516707.1:p.Asp1077Asn", "hgvsWellDefined": "XP_011516707.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS544906" }, { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518406.2:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_011516708.1:p.Asp1077Asn", "hgvsWellDefined": "XP_011516708.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS544907" }, { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XM_011518408.3:c.3229G>A" ], "proteinEffect": { "hgvs": "XP_011516710.1:p.Asp1077Asn", "hgvsWellDefined": "XP_011516710.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS544908" }, { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XR_001746251.1:n.3413G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS594602" }, { "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "XR_929739.2:n.3413G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS609274" }, { "@id": "http://reg.genome.network/allele/PA658662228", "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_015046.7:c.3229G>A" ], "proteinEffect": { "hgvs": "NP_055861.3:p.Asp1077Asn", "hgvsWellDefined": "NP_055861.3:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS668612", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000224140.6:c.3229G>A" }, "RefSeq": { "hgvs": "NM_015046.7:c.3229G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000224140.5:p.Asp1077Asn" }, "RefSeq": { "hgvs": "NP_055861.3:p.Asp1077Asn" } } } }, { "@id": "http://reg.genome.network/allele/PA2827617841", "coordinates": [ { "allele": "A", "end": 3413, "referenceAllele": "G", "start": 3412 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_001351528.2:c.3229G>A" ], "proteinEffect": { "hgvs": "NP_001338457.1:p.Asp1077Asn", "hgvsWellDefined": "NP_001338457.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS688870" }, { "@id": "http://reg.genome.network/allele/PA2827616512", "coordinates": [ { "allele": "A", "end": 3549, "referenceAllele": "G", "start": 3548 } ], "gene": "http://reg.genome.network/gene/GN000445", "geneNCBI_id": 23064, "geneSymbol": "SETX", "hgvs": [ "NM_001351527.2:c.3229G>A" ], "proteinEffect": { "hgvs": "NP_001338456.1:p.Asp1077Asn", "hgvsWellDefined": "NP_001338456.1:p.Asp1077Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS719848" } ], "type": "nucleotide" }