{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA16602472", "communityStandardTitle": [ "NM_005359.6(SMAD4):c.1065C>A (p.Asp355Glu)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=14095", "active": true, "id": "COSM14095" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=362878[alleleid]", "alleleId": 362878, "preferredName": "NM_005359.6(SMAD4):c.1065C>A (p.Asp355Glu)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/375999", "RCV": [ "RCV000435575" ], "variationId": 375999 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr18:g.48591902C>A?assembly=hg19", "id": "chr18:g.48591902C>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr18:g.51065532C>A?assembly=hg38", "id": "chr18:g.51065532C>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1057519740", "rs": 1057519740 } ] }, "genomicAlleles": [ { "chromosome": "18", "coordinates": [ { "allele": "A", "end": 51065532, "referenceAllele": "C", "start": 51065531 } ], "hgvs": [ "NC_000018.10:g.51065532C>A", "CM000680.2:g.51065532C>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000066" }, { "chromosome": "18", "coordinates": [ { "allele": "A", "end": 48591902, "referenceAllele": "C", "start": 48591901 } ], "hgvs": [ "NC_000018.9:g.48591902C>A", "CM000680.1:g.48591902C>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000042" }, { "chromosome": "18", "coordinates": [ { "allele": "A", "end": 46845900, "referenceAllele": "C", "start": 46845899 } ], "hgvs": [ "NC_000018.8:g.46845900C>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000018" }, { "coordinates": [ { "allele": "A", "end": 102493, "referenceAllele": "C", "start": 102492 } ], "hgvs": [ "NG_013013.2:g.102493C>A", "LRG_318:g.102493C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS002660" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1330, "referenceAllele": "C", "start": 1329 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000588860.6:c.1065C>A" ], "proteinEffect": { "hgvs": "ENSP00000465878.2:p.Asp355Glu", "hgvsWellDefined": "ENSP00000465878.2:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS914337" }, { "coordinates": [ { "allele": "A", "end": 1369, "referenceAllele": "C", "start": 1368 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000589076.6:c.1065C>A" ], "proteinEffect": { "hgvs": "ENSP00000466934.2:p.Asp355Glu", "hgvsWellDefined": "ENSP00000466934.2:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS914338" }, { "coordinates": [ { "allele": "A", "end": 1772, "referenceAllele": "C", "start": 1771 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000589941.2:c.1065C>A" ], "proteinEffect": { "hgvs": "ENSP00000465874.2:p.Asp355Glu", "hgvsWellDefined": "ENSP00000465874.2:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS914340" }, { "coordinates": [ { "allele": "A", "end": 1188, "referenceAllele": "C", "start": 1187 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000590061.2:c.1065C>A" ], "proteinEffect": { "hgvs": "ENSP00000464772.2:p.Asp355Glu", "hgvsWellDefined": "ENSP00000464772.2:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS914342" }, { "coordinates": [ { "allele": "A", "end": 1597, "referenceAllele": "C", "start": 1596 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000593223.2:c.1065C>A" ], "proteinEffect": { "hgvs": "ENSP00000466118.2:p.Asp355Glu", "hgvsWellDefined": "ENSP00000466118.2:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS914349" }, { "coordinates": [ { "allele": "A", "end": 1192, "referenceAllele": "C", "start": 1191 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000611848.2:c.1065C>A" ], "proteinEffect": { "hgvs": "ENSP00000478613.2:p.Asp355Glu", "hgvsWellDefined": "ENSP00000478613.2:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS826412" }, { "coordinates": [ { "allele": "A", "end": 2437, "referenceAllele": "C", "start": 2436 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000684953.1:n.2437C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS829809" }, { "coordinates": [ { "allele": "A", "end": 1516, "referenceAllele": "C", "start": 1515 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000685090.1:n.1516C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS829875" }, { "coordinates": [ { "allele": "A", "end": 1173, "referenceAllele": "C", "start": 1172 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000685232.1:n.1173C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS829955" }, { "coordinates": [ { "allele": "A", "end": 316, "referenceAllele": "C", "start": 315 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000688307.1:n.316C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS831552" }, { "coordinates": [ { "allele": "A", "end": 1173, "referenceAllele": "C", "start": 1172 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000688574.1:n.1173C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS831698" }, { "coordinates": [ { "allele": "A", "end": 1279, "referenceAllele": "C", "start": 1278 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000688903.1:n.1279C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS831880" }, { "coordinates": [ { "allele": "A", "end": 2547, "referenceAllele": "C", "start": 2546 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000691124.1:n.2547C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS833056" }, { "coordinates": [ { "allele": "A", "end": 1603, "referenceAllele": "C", "start": 1602 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000342988.8:c.1065C>A" ], "proteinEffect": { "hgvs": "ENSP00000341551.3:p.Asp355Glu", "hgvsWellDefined": "ENSP00000341551.3:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS748110", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000342988.8:c.1065C>A" }, "RefSeq": { "hgvs": "NM_005359.6:c.1065C>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000341551.3:p.Asp355Glu" }, "RefSeq": { "hgvs": "NP_005350.1:p.Asp355Glu" } } } }, { "coordinates": [ { "allele": "A", "end": 1603, "referenceAllele": "C", "start": 1602 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000342988.7:c.1065C>A" ], "proteinEffect": { "hgvs": "ENSP00000341551.3:p.Asp355Glu", "hgvsWellDefined": "ENSP00000341551.3:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS261669" }, { "coordinates": [ { "allele": "A", "end": 1323, "referenceAllele": "C", "start": 1322 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000398417.6:c.1065C>A" ], "proteinEffect": { "hgvs": "ENSP00000381452.1:p.Asp355Glu", "hgvsWellDefined": "ENSP00000381452.1:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS278258" }, { "coordinates": [ { "allele": "A", "end": 777, "referenceAllele": "C", "start": 776 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000588745.5:c.777C>A" ], "proteinEffect": { "hgvs": "ENSP00000464901.1:p.Asp259Glu", "hgvsWellDefined": "ENSP00000464901.1:p.Asp259Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS390999" }, { "coordinates": [ { "allele": "A", "end": 3066, "referenceAllele": "C", "start": 3065 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000591126.5:n.3066C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS392668" }, { "coordinates": [ { "allele": "A", "end": 955, "endIntronDirection": "+", "endIntronOffset": 5616, "referenceAllele": "C", "start": 955, "startIntronDirection": "+", "startIntronOffset": 5615 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000592186.5:c.955+5616C>A" ], "proteinEffect": { "hgvs": "ENSP00000468611.1:n.955+5616C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS393389" }, { "coordinates": [ { "allele": "A", "end": 265, "referenceAllele": "C", "start": 264 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000611848.1:c.265C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS401041" }, { "@id": "http://reg.genome.network/allele/PA645474855", "coordinates": [ { "allele": "A", "end": 1603, "referenceAllele": "C", "start": 1602 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "NM_005359.5:c.1065C>A", "LRG_318t1:c.1065C>A" ], "proteinEffect": { "hgvs": "NP_005350.1:p.Asp355Glu", "hgvsWellDefined": "NP_005350.1:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS030461" }, { "@id": "http://reg.genome.network/allele/PA645474855", "coordinates": [ { "allele": "A", "end": 1603, "referenceAllele": "C", "start": 1602 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "NM_005359.6:c.1065C>A" ], "proteinEffect": { "hgvs": "NP_005350.1:p.Asp355Glu", "hgvsWellDefined": "NP_005350.1:p.Asp355Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS696402", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000342988.8:c.1065C>A" }, "RefSeq": { "hgvs": "NM_005359.6:c.1065C>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000341551.3:p.Asp355Glu" }, "RefSeq": { "hgvs": "NP_005350.1:p.Asp355Glu" } } } } ], "type": "nucleotide" }