{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA2097738", "communityStandardTitle": [ "NM_014140.4(SMARCAL1):c.926G>A (p.Ser309Asn)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1927034[alleleid]", "alleleId": 1927034, "preferredName": "NM_014140.4(SMARCAL1):c.926G>A (p.Ser309Asn)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/2197453", "RCV": [ "RCV002637706", "RCV003341516" ], "variationId": 2197453 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/2-217285085-G-A", "id": "2-217285085-G-A", "variant": "2:217285085 G / A" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.217285085G>A?assembly=hg19", "id": "chr2:g.217285085G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.216420362G>A?assembly=hg38", "id": "chr2:g.216420362G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/545116067", "rs": 545116067 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-217285085-G-A?dataset=gnomad_r2_1", "id": "2-217285085-G-A", "variant": "2:217285085 G / A" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-216420362-G-A?dataset=gnomad_r3", "id": "2-216420362-G-A", "variant": "2:216420362 G / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-216420362-G-A?dataset=gnomad_r4", "id": "2-216420362-G-A", "variant": "2:216420362 G / A" } ] }, "genomicAlleles": [ { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 216420362, "referenceAllele": "G", "start": 216420361 } ], "hgvs": [ "NC_000002.12:g.216420362G>A", "CM000664.2:g.216420362G>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000050" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 217285085, "referenceAllele": "G", "start": 217285084 } ], "hgvs": [ "NC_000002.11:g.217285085G>A", "CM000664.1:g.217285085G>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000026" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 216993330, "referenceAllele": "G", "start": 216993329 } ], "hgvs": [ "NC_000002.10:g.216993330G>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000002" }, { "coordinates": [ { "allele": "A", "end": 12949, "referenceAllele": "G", "start": 12948 } ], "hgvs": [ "NG_009771.1:g.12949G>A", "LRG_108:g.12949G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001631" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1178, "referenceAllele": "G", "start": 1177 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000425815.6:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000394410.2:p.Ser309Asn", "hgvsWellDefined": "ENSP00000394410.2:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS904799" }, { "coordinates": [ { "allele": "A", "end": 1211, "referenceAllele": "G", "start": 1210 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000430374.6:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000405077.2:p.Ser309Asn", "hgvsWellDefined": "ENSP00000405077.2:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS904832" }, { "coordinates": [ { "allele": "A", "end": 1246, "referenceAllele": "G", "start": 1245 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000444508.6:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000398969.2:p.Ser309Asn", "hgvsWellDefined": "ENSP00000398969.2:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS904940" }, { "coordinates": [ { "allele": "A", "end": 1287, "referenceAllele": "G", "start": 1286 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697898.1:n.1287G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS909056" }, { "coordinates": [ { "allele": "A", "end": 1147, "endIntronDirection": "-", "endIntronOffset": 3270, "referenceAllele": "G", "start": 1147, "startIntronDirection": "-", "startIntronOffset": 3271 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697899.1:c.863-3271G>A" ], "proteinEffect": { "hgvs": "ENSP00000513470.1:n.863-3271G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS909057" }, { "coordinates": [ { "allele": "A", "end": 1202, "referenceAllele": "G", "start": 1201 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697900.1:n.1202G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS909058" }, { "coordinates": [ { "allele": "A", "end": 1160, "referenceAllele": "G", "start": 1159 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697901.1:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000513471.1:p.Ser309Asn", "hgvsWellDefined": "ENSP00000513471.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS909059" }, { "coordinates": [ { "allele": "A", "end": 1158, "referenceAllele": "G", "start": 1157 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697902.1:n.1158G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS909060" }, { "coordinates": [ { "allele": "A", "end": 1158, "referenceAllele": "G", "start": 1157 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697903.1:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000513472.1:p.Ser309Asn", "hgvsWellDefined": "ENSP00000513472.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS909061" }, { "coordinates": [ { "allele": "A", "end": 1086, "referenceAllele": "G", "start": 1085 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697904.1:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000513473.1:p.Ser309Asn", "hgvsWellDefined": "ENSP00000513473.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS909062" }, { "coordinates": [ { "allele": "A", "end": 1122, "referenceAllele": "G", "start": 1121 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697905.1:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000513474.1:p.Ser309Asn", "hgvsWellDefined": "ENSP00000513474.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS909063" }, { "coordinates": [ { "allele": "A", "end": 1006, "endIntronDirection": "-", "endIntronOffset": 3270, "referenceAllele": "G", "start": 1006, "startIntronDirection": "-", "startIntronOffset": 3271 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697906.1:c.863-3271G>A" ], "proteinEffect": { "hgvs": "ENSP00000513475.1:n.863-3271G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS909064" }, { "coordinates": [ { "allele": "A", "end": 1052, "referenceAllele": "G", "start": 1051 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697907.1:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000513476.1:p.Ser309Asn", "hgvsWellDefined": "ENSP00000513476.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS909065" }, { "coordinates": [ { "allele": "A", "end": 1186, "referenceAllele": "G", "start": 1185 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000357276.9:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000349823.4:p.Ser309Asn", "hgvsWellDefined": "ENSP00000349823.4:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS748922", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000357276.9:c.926G>A" }, "RefSeq": { "hgvs": "NM_014140.4:c.926G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000349823.4:p.Ser309Asn" }, "RefSeq": { "hgvs": "NP_054859.2:p.Ser309Asn" } } } }, { "coordinates": [ { "allele": "A", "end": 1256, "referenceAllele": "G", "start": 1255 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000357276.8:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000349823.4:p.Ser309Asn", "hgvsWellDefined": "ENSP00000349823.4:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS264043" }, { "coordinates": [ { "allele": "A", "end": 1077, "referenceAllele": "G", "start": 1076 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000358207.9:c.926G>A" ], "proteinEffect": { "hgvs": "ENSP00000350940.5:p.Ser309Asn", "hgvsWellDefined": "ENSP00000350940.5:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS264375" }, { "coordinates": [ { "allele": "A", "end": 518, "referenceAllele": "G", "start": 517 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000392128.6:c.518G>A" ], "proteinEffect": { "hgvs": "ENSP00000375974.2:p.Ser173Asn", "hgvsWellDefined": "ENSP00000375974.2:p.Ser173Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS274936" }, { "coordinates": [ { "allele": "A", "end": 200, "referenceAllele": "G", "start": 199 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000412913.1:c.86G>A" ], "proteinEffect": { "hgvs": "ENSP00000390248.1:p.Ser29Asn", "hgvsWellDefined": "ENSP00000390248.1:p.Ser29Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS282826" }, { "coordinates": [ { "allele": "A", "end": 623, "referenceAllele": "G", "start": 622 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000427645.5:c.623G>A" ], "proteinEffect": { "hgvs": "ENSP00000392997.1:p.Ser208Asn", "hgvsWellDefined": "ENSP00000392997.1:p.Ser208Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS289800" }, { "@id": "http://reg.genome.network/allele/PA2825629747", "coordinates": [ { "allele": "A", "end": 1070, "referenceAllele": "G", "start": 1069 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "NM_001127207.1:c.926G>A" ], "proteinEffect": { "hgvs": "NP_001120679.1:p.Ser309Asn", "hgvsWellDefined": "NP_001120679.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS011543" }, { "@id": "http://reg.genome.network/allele/PA2580368445", "coordinates": [ { "allele": "A", "end": 1256, "referenceAllele": "G", "start": 1255 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "NM_014140.3:c.926G>A", "LRG_108t1:c.926G>A" ], "proteinEffect": { "hgvs": "NP_054859.2:p.Ser309Asn", "hgvsWellDefined": "NP_054859.2:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS032934" }, { "coordinates": [ { "allele": "A", "end": 1194, "referenceAllele": "G", "start": 1193 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_005246631.2:c.926G>A" ], "proteinEffect": { "hgvs": "XP_005246688.1:p.Ser309Asn", "hgvsWellDefined": "XP_005246688.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS057716" }, { "coordinates": [ { "allele": "A", "end": 1246, "referenceAllele": "G", "start": 1245 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_005246632.1:c.926G>A" ], "proteinEffect": { "hgvs": "XP_005246689.1:p.Ser309Asn", "hgvsWellDefined": "XP_005246689.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS057717" }, { "coordinates": [ { "allele": "A", "end": 1239, "referenceAllele": "G", "start": 1238 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_006712557.1:c.926G>A" ], "proteinEffect": { "hgvs": "XP_006712620.1:p.Ser309Asn", "hgvsWellDefined": "XP_006712620.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS069710" }, { "coordinates": [ { "allele": "A", "end": 1187, "referenceAllele": "G", "start": 1186 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_005246632.2:c.926G>A" ], "proteinEffect": { "hgvs": "XP_005246689.1:p.Ser309Asn", "hgvsWellDefined": "XP_005246689.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS532654" }, { "coordinates": [ { "allele": "A", "end": 1044, "referenceAllele": "G", "start": 1043 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_017004228.2:c.10G>A" ], "proteinEffect": { "hgvs": "XP_016859717.1:p.Ala4Thr", "hgvsWellDefined": "XP_016859717.1:p.Ala4Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS559780" }, { "@id": "http://reg.genome.network/allele/PA2825629747", "coordinates": [ { "allele": "A", "end": 1055, "referenceAllele": "G", "start": 1054 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "NM_001127207.2:c.926G>A" ], "proteinEffect": { "hgvs": "NP_001120679.1:p.Ser309Asn", "hgvsWellDefined": "NP_001120679.1:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS676852" }, { "@id": "http://reg.genome.network/allele/PA2580368445", "coordinates": [ { "allele": "A", "end": 1186, "referenceAllele": "G", "start": 1185 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "NM_014140.4:c.926G>A" ], "proteinEffect": { "hgvs": "NP_054859.2:p.Ser309Asn", "hgvsWellDefined": "NP_054859.2:p.Ser309Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS697187", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000357276.9:c.926G>A" }, "RefSeq": { "hgvs": "NM_014140.4:c.926G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000349823.4:p.Ser309Asn" }, "RefSeq": { "hgvs": "NP_054859.2:p.Ser309Asn" } } } } ], "type": "nucleotide" }