{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA2097766", "communityStandardTitle": [ "NM_014140.4(SMARCAL1):c.1069T>A (p.Phe357Ile)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=629441[alleleid]", "alleleId": 629441, "preferredName": "NM_014140.4(SMARCAL1):c.1069T>A (p.Phe357Ile)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/664419", "RCV": [ "RCV000822517" ], "variationId": 664419 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/2-217285228-T-A", "id": "2-217285228-T-A", "variant": "2:217285228 T / A" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.217285228T>A?assembly=hg19", "id": "chr2:g.217285228T>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.216420505T>A?assembly=hg38", "id": "chr2:g.216420505T>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/369180164", "rs": 369180164 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-217285228-T-A?dataset=gnomad_r2_1", "id": "2-217285228-T-A", "variant": "2:217285228 T / A" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-216420505-T-A?dataset=gnomad_r3", "id": "2-216420505-T-A", "variant": "2:216420505 T / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-216420505-T-A?dataset=gnomad_r4", "id": "2-216420505-T-A", "variant": "2:216420505 T / A" } ] }, "genomicAlleles": [ { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 216420505, "referenceAllele": "T", "start": 216420504 } ], "hgvs": [ "NC_000002.12:g.216420505T>A", "CM000664.2:g.216420505T>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000050" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 217285228, "referenceAllele": "T", "start": 217285227 } ], "hgvs": [ "NC_000002.11:g.217285228T>A", "CM000664.1:g.217285228T>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000026" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 216993473, "referenceAllele": "T", "start": 216993472 } ], "hgvs": [ "NC_000002.10:g.216993473T>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000002" }, { "coordinates": [ { "allele": "A", "end": 13092, "referenceAllele": "T", "start": 13091 } ], "hgvs": [ "NG_009771.1:g.13092T>A", "LRG_108:g.13092T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001631" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1321, "referenceAllele": "T", "start": 1320 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000425815.6:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000394410.2:p.Phe357Ile", "hgvsWellDefined": "ENSP00000394410.2:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS904799" }, { "coordinates": [ { "allele": "A", "end": 1354, "referenceAllele": "T", "start": 1353 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000430374.6:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000405077.2:p.Phe357Ile", "hgvsWellDefined": "ENSP00000405077.2:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS904832" }, { "coordinates": [ { "allele": "A", "end": 1389, "referenceAllele": "T", "start": 1388 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000444508.6:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000398969.2:p.Phe357Ile", "hgvsWellDefined": "ENSP00000398969.2:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS904940" }, { "coordinates": [ { "allele": "A", "end": 1430, "referenceAllele": "T", "start": 1429 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697898.1:n.1430T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS909056" }, { "coordinates": [ { "allele": "A", "end": 1147, "endIntronDirection": "-", "endIntronOffset": 3127, "referenceAllele": "T", "start": 1147, "startIntronDirection": "-", "startIntronOffset": 3128 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697899.1:c.863-3128T>A" ], "proteinEffect": { "hgvs": "ENSP00000513470.1:n.863-3128T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS909057" }, { "coordinates": [ { "allele": "A", "end": 1345, "referenceAllele": "T", "start": 1344 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697900.1:n.1345T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS909058" }, { "coordinates": [ { "allele": "A", "end": 1303, "referenceAllele": "T", "start": 1302 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697901.1:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000513471.1:p.Phe357Ile", "hgvsWellDefined": "ENSP00000513471.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS909059" }, { "coordinates": [ { "allele": "A", "end": 1301, "referenceAllele": "T", "start": 1300 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697902.1:n.1301T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS909060" }, { "coordinates": [ { "allele": "A", "end": 1301, "referenceAllele": "T", "start": 1300 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697903.1:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000513472.1:p.Phe357Ile", "hgvsWellDefined": "ENSP00000513472.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS909061" }, { "coordinates": [ { "allele": "A", "end": 1229, "referenceAllele": "T", "start": 1228 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697904.1:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000513473.1:p.Phe357Ile", "hgvsWellDefined": "ENSP00000513473.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS909062" }, { "coordinates": [ { "allele": "A", "end": 1265, "referenceAllele": "T", "start": 1264 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697905.1:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000513474.1:p.Phe357Ile", "hgvsWellDefined": "ENSP00000513474.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS909063" }, { "coordinates": [ { "allele": "A", "end": 1006, "endIntronDirection": "-", "endIntronOffset": 3127, "referenceAllele": "T", "start": 1006, "startIntronDirection": "-", "startIntronOffset": 3128 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697906.1:c.863-3128T>A" ], "proteinEffect": { "hgvs": "ENSP00000513475.1:n.863-3128T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS909064" }, { "coordinates": [ { "allele": "A", "end": 1195, "referenceAllele": "T", "start": 1194 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000697907.1:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000513476.1:p.Phe357Ile", "hgvsWellDefined": "ENSP00000513476.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS909065" }, { "coordinates": [ { "allele": "A", "end": 1329, "referenceAllele": "T", "start": 1328 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000357276.9:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000349823.4:p.Phe357Ile", "hgvsWellDefined": "ENSP00000349823.4:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS748922", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000357276.9:c.1069T>A" }, "RefSeq": { "hgvs": "NM_014140.4:c.1069T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000349823.4:p.Phe357Ile" }, "RefSeq": { "hgvs": "NP_054859.2:p.Phe357Ile" } } } }, { "coordinates": [ { "allele": "A", "end": 1399, "referenceAllele": "T", "start": 1398 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000357276.8:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000349823.4:p.Phe357Ile", "hgvsWellDefined": "ENSP00000349823.4:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS264043" }, { "coordinates": [ { "allele": "A", "end": 1220, "referenceAllele": "T", "start": 1219 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000358207.9:c.1069T>A" ], "proteinEffect": { "hgvs": "ENSP00000350940.5:p.Phe357Ile", "hgvsWellDefined": "ENSP00000350940.5:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS264375" }, { "coordinates": [ { "allele": "A", "end": 661, "referenceAllele": "T", "start": 660 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000392128.6:c.661T>A" ], "proteinEffect": { "hgvs": "ENSP00000375974.2:p.Phe221Ile", "hgvsWellDefined": "ENSP00000375974.2:p.Phe221Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS274936" }, { "coordinates": [ { "allele": "A", "end": 343, "referenceAllele": "T", "start": 342 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000412913.1:c.229T>A" ], "proteinEffect": { "hgvs": "ENSP00000390248.1:p.Phe77Ile", "hgvsWellDefined": "ENSP00000390248.1:p.Phe77Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS282826" }, { "coordinates": [ { "allele": "A", "end": 766, "referenceAllele": "T", "start": 765 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "ENST00000427645.5:c.766T>A" ], "proteinEffect": { "hgvs": "ENSP00000392997.1:p.Phe256Ile", "hgvsWellDefined": "ENSP00000392997.1:p.Phe256Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS289800" }, { "@id": "http://reg.genome.network/allele/PA2825629806", "coordinates": [ { "allele": "A", "end": 1213, "referenceAllele": "T", "start": 1212 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "NM_001127207.1:c.1069T>A" ], "proteinEffect": { "hgvs": "NP_001120679.1:p.Phe357Ile", "hgvsWellDefined": "NP_001120679.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS011543" }, { "@id": "http://reg.genome.network/allele/PA916010831", "coordinates": [ { "allele": "A", "end": 1399, "referenceAllele": "T", "start": 1398 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "NM_014140.3:c.1069T>A", "LRG_108t1:c.1069T>A" ], "proteinEffect": { "hgvs": "NP_054859.2:p.Phe357Ile", "hgvsWellDefined": "NP_054859.2:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS032934" }, { "coordinates": [ { "allele": "A", "end": 1337, "referenceAllele": "T", "start": 1336 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_005246631.2:c.1069T>A" ], "proteinEffect": { "hgvs": "XP_005246688.1:p.Phe357Ile", "hgvsWellDefined": "XP_005246688.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS057716" }, { "coordinates": [ { "allele": "A", "end": 1389, "referenceAllele": "T", "start": 1388 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_005246632.1:c.1069T>A" ], "proteinEffect": { "hgvs": "XP_005246689.1:p.Phe357Ile", "hgvsWellDefined": "XP_005246689.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS057717" }, { "coordinates": [ { "allele": "A", "end": 1382, "referenceAllele": "T", "start": 1381 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_006712557.1:c.1069T>A" ], "proteinEffect": { "hgvs": "XP_006712620.1:p.Phe357Ile", "hgvsWellDefined": "XP_006712620.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS069710" }, { "coordinates": [ { "allele": "A", "end": 1330, "referenceAllele": "T", "start": 1329 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_005246632.2:c.1069T>A" ], "proteinEffect": { "hgvs": "XP_005246689.1:p.Phe357Ile", "hgvsWellDefined": "XP_005246689.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS532654" }, { "coordinates": [ { "allele": "A", "end": 1187, "referenceAllele": "T", "start": 1186 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "XM_017004228.2:c.153T>A" ], "proteinEffect": { "hgvs": "XP_016859717.1:p.Phe51Leu", "hgvsWellDefined": "XP_016859717.1:p.Phe51Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS559780" }, { "@id": "http://reg.genome.network/allele/PA2825629806", "coordinates": [ { "allele": "A", "end": 1198, "referenceAllele": "T", "start": 1197 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "NM_001127207.2:c.1069T>A" ], "proteinEffect": { "hgvs": "NP_001120679.1:p.Phe357Ile", "hgvsWellDefined": "NP_001120679.1:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS676852" }, { "@id": "http://reg.genome.network/allele/PA916010831", "coordinates": [ { "allele": "A", "end": 1329, "referenceAllele": "T", "start": 1328 } ], "gene": "http://reg.genome.network/gene/GN011102", "geneNCBI_id": 50485, "geneSymbol": "SMARCAL1", "hgvs": [ "NM_014140.4:c.1069T>A" ], "proteinEffect": { "hgvs": "NP_054859.2:p.Phe357Ile", "hgvsWellDefined": "NP_054859.2:p.Phe357Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS697187", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000357276.9:c.1069T>A" }, "RefSeq": { "hgvs": "NM_014140.4:c.1069T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000349823.4:p.Phe357Ile" }, "RefSeq": { "hgvs": "NP_054859.2:p.Phe357Ile" } } } } ], "type": "nucleotide" }