{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA018551", "communityStandardTitle": [ "NM_000335.5(SCN5A):c.4780G>A (p.Asp1594Asn)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=5399235", "active": true, "id": "COSM5399235" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=5399236", "active": true, "id": "COSM5399236" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=5399237", "active": true, "id": "COSM5399237" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=24424[alleleid]", "alleleId": 24424, "preferredName": "NM_000335.5(SCN5A):c.4780G>A (p.Asp1594Asn)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/9385", "RCV": [ "RCV000009983", "RCV000058705", "RCV000183084", "RCV001329632", "RCV004528098" ], "variationId": 9385 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr3:g.38595800C>T?assembly=hg19", "id": "chr3:g.38595800C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr3:g.38554309C>T?assembly=hg38", "id": "chr3:g.38554309C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/137854607", "rs": 137854607 } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/3-38554309-C-T?dataset=gnomad_r4", "id": "3-38554309-C-T", "variant": "3:38554309 C / T" } ] }, "genomicAlleles": [ { "chromosome": "3", "coordinates": [ { "allele": "T", "end": 38554309, "referenceAllele": "C", "start": 38554308 } ], "hgvs": [ "NC_000003.12:g.38554309C>T", "CM000665.2:g.38554309C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000051" }, { "chromosome": "3", "coordinates": [ { "allele": "T", "end": 38595800, "referenceAllele": "C", "start": 38595799 } ], "hgvs": [ "NC_000003.11:g.38595800C>T", "CM000665.1:g.38595800C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000027" }, { "chromosome": "3", "coordinates": [ { "allele": "T", "end": 38570804, "referenceAllele": "C", "start": 38570803 } ], "hgvs": [ "NC_000003.10:g.38570804C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000003" }, { "coordinates": [ { "allele": "A", "end": 100364, "referenceAllele": "G", "start": 100363 } ], "hgvs": [ "NG_008934.1:g.100364G>A", "LRG_289:g.100364G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001312" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 4918, "referenceAllele": "G", "start": 4917 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000327956.7:c.4780G>A" ], "proteinEffect": { "hgvs": "ENSP00000333674.7:p.Asp1594Asn", "hgvsWellDefined": "ENSP00000333674.7:p.Asp1594Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS913961" }, { "coordinates": [ { "allele": "A", "end": 4992, "referenceAllele": "G", "start": 4991 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000333535.9:c.4783G>A" ], "proteinEffect": { "hgvs": "ENSP00000328968.4:p.Asp1595Asn", "hgvsWellDefined": "ENSP00000328968.4:p.Asp1595Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS747320" }, { "coordinates": [ { "allele": "A", "end": 4992, "referenceAllele": "G", "start": 4991 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000413689.6:c.4783G>A" ], "proteinEffect": { "hgvs": "ENSP00000410257.1:p.Asp1595Asn", "hgvsWellDefined": "ENSP00000410257.1:p.Asp1595Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS754540", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Plus Clinical", "nucleotide": { "Ensembl": { "hgvs": "ENST00000413689.6:c.4783G>A" }, "RefSeq": { "hgvs": "NM_001099404.2:c.4783G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000410257.1:p.Asp1595Asn" }, "RefSeq": { "hgvs": "NP_001092874.1:p.Asp1595Asn" } } } }, { "coordinates": [ { "allele": "A", "end": 4989, "referenceAllele": "G", "start": 4988 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000423572.7:c.4780G>A" ], "proteinEffect": { "hgvs": "ENSP00000398266.2:p.Asp1594Asn", "hgvsWellDefined": "ENSP00000398266.2:p.Asp1594Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS754985", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000423572.7:c.4780G>A" }, "RefSeq": { "hgvs": "NM_000335.5:c.4780G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000398266.2:p.Asp1594Asn" }, "RefSeq": { "hgvs": "NP_000326.2:p.Asp1594Asn" } } } }, { "coordinates": [ { "allele": "A", "end": 4933, "referenceAllele": "G", "start": 4932 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000333535.8:c.4783G>A" ], "proteinEffect": { "hgvs": "ENSP00000328968.4:p.Asp1595Asn", "hgvsWellDefined": "ENSP00000328968.4:p.Asp1595Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS247329" }, { "coordinates": [ { "allele": "A", "end": 4977, "referenceAllele": "G", "start": 4976 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000413689.5:c.4783G>A" ], "proteinEffect": { "hgvs": "ENSP00000410257.1:p.Asp1595Asn", "hgvsWellDefined": "ENSP00000410257.1:p.Asp1595Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS247165" }, { "coordinates": [ { "allele": "A", "end": 4771, "referenceAllele": "G", "start": 4770 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000414099.6:c.4729G>A" ], "proteinEffect": { "hgvs": "ENSP00000398962.2:p.Asp1577Asn", "hgvsWellDefined": "ENSP00000398962.2:p.Asp1577Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS247373" }, { "coordinates": [ { "allele": "A", "end": 4835, "referenceAllele": "G", "start": 4834 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000423572.6:c.4780G>A" ], "proteinEffect": { "hgvs": "ENSP00000398266.2:p.Asp1594Asn", "hgvsWellDefined": "ENSP00000398266.2:p.Asp1594Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS247184" }, { "coordinates": [ { "allele": "A", "end": 4923, "referenceAllele": "G", "start": 4922 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000425664.5:c.4729G>A" ], "proteinEffect": { "hgvs": "ENSP00000416634.1:p.Asp1577Asn", "hgvsWellDefined": "ENSP00000416634.1:p.Asp1577Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS246629" }, { "coordinates": [ { "allele": "A", "end": 4630, "referenceAllele": "G", "start": 4629 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000449557.6:c.4621G>A" ], "proteinEffect": { "hgvs": "ENSP00000413996.2:p.Asp1541Asn", "hgvsWellDefined": "ENSP00000413996.2:p.Asp1541Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS247361" }, { "coordinates": [ { "allele": "A", "end": 4663, "referenceAllele": "G", "start": 4662 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000450102.6:c.4621G>A" ], "proteinEffect": { "hgvs": "ENSP00000403355.2:p.Asp1541Asn", "hgvsWellDefined": "ENSP00000403355.2:p.Asp1541Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS247217" }, { "coordinates": [ { "allele": "A", "end": 4816, "referenceAllele": "G", "start": 4815 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000451551.6:c.4621G>A" ], "proteinEffect": { "hgvs": "ENSP00000388797.2:p.Asp1541Asn", "hgvsWellDefined": "ENSP00000388797.2:p.Asp1541Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS247201" }, { "coordinates": [ { "allele": "A", "end": 4739, "endIntronDirection": "+", "endIntronOffset": 66, "referenceAllele": "G", "start": 4739, "startIntronDirection": "+", "startIntronOffset": 65 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000455624.6:c.4714+66G>A" ], "proteinEffect": { "hgvs": "ENSP00000399524.2:n.4714+66G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS247378" }, { "coordinates": [ { "allele": "A", "end": 241, "referenceAllele": "G", "start": 240 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "ENST00000464652.1:n.241G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS308431" }, { "@id": "http://reg.genome.network/allele/PA120336", "coordinates": [ { "allele": "A", "end": 4974, "referenceAllele": "G", "start": 4973 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_000335.4:c.4780G>A", "LRG_289t2:c.4780G>A" ], "proteinEffect": { "hgvs": "NP_000326.2:p.Asp1594Asn", "hgvsWellDefined": "NP_000326.2:p.Asp1594Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS006398" }, { "@id": "http://reg.genome.network/allele/PA120337", "coordinates": [ { "allele": "A", "end": 4977, "referenceAllele": "G", "start": 4976 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001099404.1:c.4783G>A", "LRG_289t3:c.4783G>A" ], "proteinEffect": { "hgvs": "NP_001092874.1:p.Asp1595Asn", "hgvsWellDefined": "NP_001092874.1:p.Asp1595Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS010738" }, { "@id": "http://reg.genome.network/allele/PA2825496500", "coordinates": [ { "allele": "A", "end": 4923, "referenceAllele": "G", "start": 4922 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001099405.1:c.4729G>A" ], "proteinEffect": { "hgvs": "NP_001092875.1:p.Asp1577Asn", "hgvsWellDefined": "NP_001092875.1:p.Asp1577Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS010739" }, { "coordinates": [ { "allele": "A", "end": 4909, "endIntronDirection": "+", "endIntronOffset": 66, "referenceAllele": "G", "start": 4909, "startIntronDirection": "+", "startIntronOffset": 65 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001160160.1:c.4714+66G>A" ], "proteinEffect": { "hgvs": "NP_001153632.1:n.4714+66G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS014136" }, { "@id": "http://reg.genome.network/allele/PA2825945265", "coordinates": [ { "allele": "A", "end": 4816, "referenceAllele": "G", "start": 4815 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001160161.1:c.4621G>A" ], "proteinEffect": { "hgvs": "NP_001153633.1:p.Asp1541Asn", "hgvsWellDefined": "NP_001153633.1:p.Asp1541Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS014137" }, { "@id": "http://reg.genome.network/allele/PA107646", "coordinates": [ { "allele": "A", "end": 4977, "referenceAllele": "G", "start": 4976 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_198056.2:c.4783G>A", "LRG_289t1:c.4783G>A" ], "proteinEffect": { "hgvs": "NP_932173.1:p.Asp1595Asn", "hgvsWellDefined": "NP_932173.1:p.Asp1595Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS044407" }, { "coordinates": [ { "allele": "A", "end": 4915, "referenceAllele": "G", "start": 4914 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "XM_006713282.2:c.4783G>A" ], "proteinEffect": { "hgvs": "XP_006713345.1:p.Asp1595Asn", "hgvsWellDefined": "XP_006713345.1:p.Asp1595Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS070082" }, { "coordinates": [ { "allele": "A", "end": 4969, "referenceAllele": "G", "start": 4968 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "XM_011533991.1:c.4780G>A" ], "proteinEffect": { "hgvs": "XP_011532293.1:p.Asp1594Asn", "hgvsWellDefined": "XP_011532293.1:p.Asp1594Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS101009" }, { "coordinates": [ { "allele": "A", "end": 4761, "referenceAllele": "G", "start": 4760 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "XM_011533992.1:c.4654G>A" ], "proteinEffect": { "hgvs": "XP_011532294.1:p.Asp1552Asn", "hgvsWellDefined": "XP_011532294.1:p.Asp1552Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS101010" }, { "@id": "http://reg.genome.network/allele/PA2827923512", "coordinates": [ { "allele": "A", "end": 4921, "referenceAllele": "G", "start": 4920 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001354701.1:c.4726G>A" ], "proteinEffect": { "hgvs": "NP_001341630.1:p.Asp1576Asn", "hgvsWellDefined": "NP_001341630.1:p.Asp1576Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS522627" }, { "coordinates": [ { "allele": "A", "end": 4969, "referenceAllele": "G", "start": 4968 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "XM_011533991.2:c.4780G>A" ], "proteinEffect": { "hgvs": "XP_011532293.1:p.Asp1594Asn", "hgvsWellDefined": "XP_011532293.1:p.Asp1594Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS551456" }, { "coordinates": [ { "allele": "A", "end": 4810, "referenceAllele": "G", "start": 4809 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "XM_017007017.1:c.4621G>A" ], "proteinEffect": { "hgvs": "XP_016862506.1:p.Asp1541Asn", "hgvsWellDefined": "XP_016862506.1:p.Asp1541Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS561890" }, { "@id": "http://reg.genome.network/allele/PA120336", "coordinates": [ { "allele": "A", "end": 4989, "referenceAllele": "G", "start": 4988 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_000335.5:c.4780G>A" ], "proteinEffect": { "hgvs": "NP_000326.2:p.Asp1594Asn", "hgvsWellDefined": "NP_000326.2:p.Asp1594Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS674795", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000423572.7:c.4780G>A" }, "RefSeq": { "hgvs": "NM_000335.5:c.4780G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000398266.2:p.Asp1594Asn" }, "RefSeq": { "hgvs": "NP_000326.2:p.Asp1594Asn" } } } }, { "coordinates": [ { "allele": "A", "end": 4923, "endIntronDirection": "+", "endIntronOffset": 66, "referenceAllele": "G", "start": 4923, "startIntronDirection": "+", "startIntronOffset": 65 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001160160.2:c.4714+66G>A" ], "proteinEffect": { "hgvs": "NP_001153632.1:n.4714+66G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS678128" }, { "@id": "http://reg.genome.network/allele/PA2827923512", "coordinates": [ { "allele": "A", "end": 4935, "referenceAllele": "G", "start": 4934 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001354701.2:c.4726G>A" ], "proteinEffect": { "hgvs": "NP_001341630.1:p.Asp1576Asn", "hgvsWellDefined": "NP_001341630.1:p.Asp1576Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS690293" }, { "@id": "http://reg.genome.network/allele/PA120337", "coordinates": [ { "allele": "A", "end": 4992, "referenceAllele": "G", "start": 4991 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001099404.2:c.4783G>A" ], "proteinEffect": { "hgvs": "NP_001092874.1:p.Asp1595Asn", "hgvsWellDefined": "NP_001092874.1:p.Asp1595Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS711956", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Plus Clinical", "nucleotide": { "Ensembl": { "hgvs": "ENST00000413689.6:c.4783G>A" }, "RefSeq": { "hgvs": "NM_001099404.2:c.4783G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000410257.1:p.Asp1595Asn" }, "RefSeq": { "hgvs": "NP_001092874.1:p.Asp1595Asn" } } } }, { "@id": "http://reg.genome.network/allele/PA2825496500", "coordinates": [ { "allele": "A", "end": 4938, "referenceAllele": "G", "start": 4937 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001099405.2:c.4729G>A" ], "proteinEffect": { "hgvs": "NP_001092875.1:p.Asp1577Asn", "hgvsWellDefined": "NP_001092875.1:p.Asp1577Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS711957" }, { "@id": "http://reg.genome.network/allele/PA2825945265", "coordinates": [ { "allele": "A", "end": 4830, "referenceAllele": "G", "start": 4829 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_001160161.2:c.4621G>A" ], "proteinEffect": { "hgvs": "NP_001153633.1:p.Asp1541Asn", "hgvsWellDefined": "NP_001153633.1:p.Asp1541Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS712964" }, { "@id": "http://reg.genome.network/allele/PA107646", "coordinates": [ { "allele": "A", "end": 4992, "referenceAllele": "G", "start": 4991 } ], "gene": "http://reg.genome.network/gene/GN010593", "geneNCBI_id": 6331, "geneSymbol": "SCN5A", "hgvs": [ "NM_198056.3:c.4783G>A" ], "proteinEffect": { "hgvs": "NP_932173.1:p.Asp1595Asn", "hgvsWellDefined": "NP_932173.1:p.Asp1595Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS729873" } ], "type": "nucleotide" }