{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA242443", "communityStandardTitle": [ "NM_004006.3(DMD):c.3269A>T (p.Gln1090Leu)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=5977481", "active": true, "id": "COSM5977481" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=5977482", "active": true, "id": "COSM5977482" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=5977483", "active": true, "id": "COSM5977483" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=192979[alleleid]", "alleleId": 192979, "preferredName": "NM_004006.3(DMD):c.3269A>T (p.Gln1090Leu)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/195818", "RCV": [ "RCV000176480", "RCV001257067", "RCV001832009", "RCV004537401" ], "variationId": 195818 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/X-32482710-T-A", "id": "X-32482710-T-A", "variant": "X:32482710 T / A" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chrX:g.32482710T>A?assembly=hg19", "id": "chrX:g.32482710T>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chrX:g.32464593T>A?assembly=hg38", "id": "chrX:g.32464593T>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/747239076", "rs": 747239076 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/X-32482710-T-A?dataset=gnomad_r2_1", "id": "X-32482710-T-A", "variant": "X:32482710 T / A" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/X-32464593-T-A?dataset=gnomad_r3", "id": "X-32464593-T-A", "variant": "X:32464593 T / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/X-32464593-T-A?dataset=gnomad_r4", "id": "X-32464593-T-A", "variant": "X:32464593 T / A" } ] }, "genomicAlleles": [ { "chromosome": "X", "coordinates": [ { "allele": "A", "end": 32464593, "referenceAllele": "T", "start": 32464592 } ], "hgvs": [ "NC_000023.11:g.32464593T>A", "CM000685.2:g.32464593T>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000071" }, { "chromosome": "X", "coordinates": [ { "allele": "A", "end": 32482710, "referenceAllele": "T", "start": 32482709 } ], "hgvs": [ "NC_000023.10:g.32482710T>A", "CM000685.1:g.32482710T>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000047" }, { "chromosome": "X", "coordinates": [ { "allele": "A", "end": 32392631, "referenceAllele": "T", "start": 32392630 } ], "hgvs": [ "NC_000023.9:g.32392631T>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000023" }, { "coordinates": [ { "allele": "T", "end": 880017, "referenceAllele": "A", "start": 880016 } ], "hgvs": [ "NG_012232.1:g.880017A>T", "LRG_199:g.880017A>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS002304" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "T", "end": 3476, "referenceAllele": "A", "start": 3475 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "ENST00000682899.1:n.3476A>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS827887" }, { "coordinates": [ { "allele": "T", "end": 3506, "referenceAllele": "A", "start": 3505 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "ENST00000357033.9:c.3269A>T" ], "proteinEffect": { "hgvs": "ENSP00000354923.3:p.Gln1090Leu", "hgvsWellDefined": "ENSP00000354923.3:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS748881", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000357033.9:c.3269A>T" }, "RefSeq": { "hgvs": "NM_004006.3:c.3269A>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000354923.3:p.Gln1090Leu" }, "RefSeq": { "hgvs": "NP_003997.2:p.Gln1090Leu" } } } }, { "coordinates": [ { "allele": "T", "end": 3476, "referenceAllele": "A", "start": 3475 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "ENST00000357033.8:c.3269A>T" ], "proteinEffect": { "hgvs": "ENSP00000354923.3:p.Gln1090Leu", "hgvsWellDefined": "ENSP00000354923.3:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS263955" }, { "coordinates": [ { "allele": "T", "end": 3452, "referenceAllele": "A", "start": 3451 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "ENST00000378677.6:c.3257A>T" ], "proteinEffect": { "hgvs": "ENSP00000367948.2:p.Gln1086Leu", "hgvsWellDefined": "ENSP00000367948.2:p.Gln1086Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS272146" }, { "coordinates": [ { "allele": "T", "end": 93, "endIntronDirection": "-", "endIntronOffset": 99393, "referenceAllele": "A", "start": 93, "startIntronDirection": "-", "startIntronOffset": 99394 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "ENST00000420596.5:c.94-99394A>T" ], "proteinEffect": { "hgvs": "ENSP00000399897.1:n.94-99394A>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS286388" }, { "coordinates": [ { "allele": "T", "end": 93, "endIntronDirection": "-", "endIntronOffset": 99882, "referenceAllele": "A", "start": 93, "startIntronDirection": "-", "startIntronOffset": 99883 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "ENST00000448370.5:c.94-99883A>T" ], "proteinEffect": { "hgvs": "ENSP00000388559.1:n.94-99883A>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS299700" }, { "coordinates": [ { "allele": "T", "end": 335, "endIntronDirection": "-", "endIntronOffset": 247529, "referenceAllele": "A", "start": 335, "startIntronDirection": "-", "startIntronOffset": 247530 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "ENST00000488902.5:n.336-247530A>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS327073" }, { "coordinates": [ { "allele": "T", "end": 3257, "referenceAllele": "A", "start": 3256 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "ENST00000619831.4:c.3257A>T" ], "proteinEffect": { "hgvs": "ENSP00000479270.1:p.Gln1086Leu", "hgvsWellDefined": "ENSP00000479270.1:p.Gln1086Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS404545" }, { "coordinates": [ { "allele": "T", "end": 3269, "referenceAllele": "A", "start": 3268 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "ENST00000620040.4:c.3269A>T" ], "proteinEffect": { "hgvs": "ENSP00000478150.1:p.Gln1090Leu", "hgvsWellDefined": "ENSP00000478150.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS404642" }, { "coordinates": [ { "allele": "T", "end": 3589, "referenceAllele": "A", "start": 3588 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "NM_000109.3:c.3245A>T" ], "proteinEffect": { "hgvs": "NP_000100.2:p.Gln1082Leu", "hgvsWellDefined": "NP_000100.2:p.Gln1082Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS006172" }, { "@id": "http://reg.genome.network/allele/PA242445", "coordinates": [ { "allele": "T", "end": 3513, "referenceAllele": "A", "start": 3512 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "NM_004006.2:c.3269A>T", "LRG_199t1:c.3269A>T" ], "proteinEffect": { "hgvs": "NP_003997.1:p.Gln1090Leu", "hgvsWellDefined": "NP_003997.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS029203" }, { "@id": "http://reg.genome.network/allele/PA2829490745", "coordinates": [ { "allele": "T", "end": 3520, "referenceAllele": "A", "start": 3519 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "NM_004009.3:c.3257A>T" ], "proteinEffect": { "hgvs": "NP_004000.1:p.Gln1086Leu", "hgvsWellDefined": "NP_004000.1:p.Gln1086Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS029204" }, { "@id": "http://reg.genome.network/allele/PA916001323", "coordinates": [ { "allele": "T", "end": 3603, "referenceAllele": "A", "start": 3602 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "NM_004010.3:c.2900A>T" ], "proteinEffect": { "hgvs": "NP_004001.1:p.Gln967Leu", "hgvsWellDefined": "NP_004001.1:p.Gln967Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS029205" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724468.2:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_006724531.1:p.Gln1090Leu", "hgvsWellDefined": "XP_006724531.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS075527" }, { "coordinates": [ { "allele": "T", "end": 3348, "referenceAllele": "A", "start": 3347 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724469.2:c.3245A>T" ], "proteinEffect": { "hgvs": "XP_006724532.1:p.Gln1082Leu", "hgvsWellDefined": "XP_006724532.1:p.Gln1082Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS075528" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724470.2:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_006724533.1:p.Gln1090Leu", "hgvsWellDefined": "XP_006724533.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS075529" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724471.2:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_006724534.1:p.Gln1090Leu", "hgvsWellDefined": "XP_006724534.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS075530" }, { "coordinates": [ { "allele": "T", "end": 3337, "referenceAllele": "A", "start": 3336 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724472.2:c.3140A>T" ], "proteinEffect": { "hgvs": "XP_006724535.1:p.Gln1047Leu", "hgvsWellDefined": "XP_006724535.1:p.Gln1047Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS075531" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724473.2:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_006724536.1:p.Gln1090Leu", "hgvsWellDefined": "XP_006724536.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS075532" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724474.2:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_006724537.1:p.Gln1090Leu", "hgvsWellDefined": "XP_006724537.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS075533" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724475.2:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_006724538.1:p.Gln1090Leu", "hgvsWellDefined": "XP_006724538.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS075534" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_011545467.1:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_011543769.1:p.Gln1090Leu", "hgvsWellDefined": "XP_011543769.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS112367" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_011545468.1:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_011543770.1:p.Gln1090Leu", "hgvsWellDefined": "XP_011543770.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS112368" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_011545469.1:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_011543771.1:p.Gln1090Leu", "hgvsWellDefined": "XP_011543771.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS112369" }, { "coordinates": [ { "allele": "T", "end": 3440, "referenceAllele": "A", "start": 3439 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724469.3:c.3245A>T" ], "proteinEffect": { "hgvs": "XP_006724532.1:p.Gln1082Leu", "hgvsWellDefined": "XP_006724532.1:p.Gln1082Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS540982" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724470.3:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_006724533.1:p.Gln1090Leu", "hgvsWellDefined": "XP_006724533.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS540983" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_006724474.3:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_006724537.1:p.Gln1090Leu", "hgvsWellDefined": "XP_006724537.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS540984" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_011545468.2:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_011543770.1:p.Gln1090Leu", "hgvsWellDefined": "XP_011543770.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS556096" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_017029328.1:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_016884817.1:p.Gln1090Leu", "hgvsWellDefined": "XP_016884817.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS578892" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_017029329.1:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_016884818.1:p.Gln1090Leu", "hgvsWellDefined": "XP_016884818.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS578893" }, { "coordinates": [ { "allele": "T", "end": 3466, "referenceAllele": "A", "start": 3465 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "XM_017029330.2:c.3269A>T" ], "proteinEffect": { "hgvs": "XP_016884819.1:p.Gln1090Leu", "hgvsWellDefined": "XP_016884819.1:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS578894" }, { "@id": "http://reg.genome.network/allele/PA2825072209", "coordinates": [ { "allele": "T", "end": 3368, "referenceAllele": "A", "start": 3367 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "NM_000109.4:c.3245A>T" ], "proteinEffect": { "hgvs": "NP_000100.3:p.Gln1082Leu", "hgvsWellDefined": "NP_000100.3:p.Gln1082Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS674704" }, { "@id": "http://reg.genome.network/allele/PA2829483691", "coordinates": [ { "allele": "T", "end": 3506, "referenceAllele": "A", "start": 3505 } ], "gene": "http://reg.genome.network/gene/GN002928", "geneNCBI_id": 1756, "geneSymbol": "DMD", "hgvs": [ "NM_004006.3:c.3269A>T" ], "proteinEffect": { "hgvs": "NP_003997.2:p.Gln1090Leu", "hgvsWellDefined": "NP_003997.2:p.Gln1090Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS696014", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000357033.9:c.3269A>T" }, "RefSeq": { "hgvs": "NM_004006.3:c.3269A>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000354923.3:p.Gln1090Leu" }, "RefSeq": { "hgvs": "NP_003997.2:p.Gln1090Leu" } } } } ], "type": "nucleotide" }