{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA402465803", "communityStandardTitle": [ "NM_005359.6(SMAD4):c.1495T>A (p.Cys499Ser)" ], "externalRecords": { "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr18:g.48604673T>A?assembly=hg19", "id": "chr18:g.48604673T>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr18:g.51078303T>A?assembly=hg38", "id": "chr18:g.51078303T>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1060500738", "rs": 1060500738 } ] }, "genomicAlleles": [ { "chromosome": "18", "coordinates": [ { "allele": "A", "end": 51078303, "referenceAllele": "T", "start": 51078302 } ], "hgvs": [ "NC_000018.10:g.51078303T>A", "CM000680.2:g.51078303T>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000066" }, { "chromosome": "18", "coordinates": [ { "allele": "A", "end": 48604673, "referenceAllele": "T", "start": 48604672 } ], "hgvs": [ "NC_000018.9:g.48604673T>A", "CM000680.1:g.48604673T>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000042" }, { "chromosome": "18", "coordinates": [ { "allele": "A", "end": 46858671, "referenceAllele": "T", "start": 46858670 } ], "hgvs": [ "NC_000018.8:g.46858671T>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000018" }, { "coordinates": [ { "allele": "A", "end": 115264, "referenceAllele": "T", "start": 115263 } ], "hgvs": [ "NG_013013.2:g.115264T>A", "LRG_318:g.115264T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS002660" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1760, "referenceAllele": "T", "start": 1759 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000588860.6:c.1495T>A" ], "proteinEffect": { "hgvs": "ENSP00000465878.2:p.Cys499Ser", "hgvsWellDefined": "ENSP00000465878.2:p.Cys499Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS914337" }, { "coordinates": [ { "allele": "A", "end": 1799, "referenceAllele": "T", "start": 1798 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000589076.6:c.1495T>A" ], "proteinEffect": { "hgvs": "ENSP00000466934.2:p.Cys499Ser", "hgvsWellDefined": "ENSP00000466934.2:p.Cys499Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS914338" }, { "coordinates": [ { "allele": "A", "end": 2202, "referenceAllele": "T", "start": 2201 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000589941.2:c.1495T>A" ], "proteinEffect": { "hgvs": "ENSP00000465874.2:p.Cys499Ser", "hgvsWellDefined": "ENSP00000465874.2:p.Cys499Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS914340" }, { "coordinates": [ { "allele": "A", "end": 1618, "referenceAllele": "T", "start": 1617 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000590061.2:c.1495T>A" ], "proteinEffect": { "hgvs": "ENSP00000464772.2:p.Cys499Ser", "hgvsWellDefined": "ENSP00000464772.2:p.Cys499Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS914342" }, { "coordinates": [ { "allele": "A", "end": 3506, "referenceAllele": "T", "start": 3505 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000593223.2:c.*1492T>A" ], "proteinEffect": { "hgvs": "ENSP00000466118.2:n.*1492T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS914349" }, { "coordinates": [ { "allele": "A", "end": 1735, "referenceAllele": "T", "start": 1734 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000611848.2:c.*147T>A" ], "proteinEffect": { "hgvs": "ENSP00000478613.2:n.*147T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS826412" }, { "coordinates": [ { "allele": "A", "end": 3510, "referenceAllele": "T", "start": 3509 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000684953.1:n.3510T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS829809" }, { "coordinates": [ { "allele": "A", "end": 3425, "referenceAllele": "T", "start": 3424 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000685090.1:n.3425T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS829875" }, { "coordinates": [ { "allele": "A", "end": 1716, "referenceAllele": "T", "start": 1715 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000685232.1:n.1716T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS829955" }, { "coordinates": [ { "allele": "A", "end": 1603, "referenceAllele": "T", "start": 1602 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000688574.1:n.1603T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS831698" }, { "coordinates": [ { "allele": "A", "end": 4456, "referenceAllele": "T", "start": 4455 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000691124.1:n.4456T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS833056" }, { "coordinates": [ { "allele": "A", "end": 2033, "referenceAllele": "T", "start": 2032 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000342988.8:c.1495T>A" ], "proteinEffect": { "hgvs": "ENSP00000341551.3:p.Cys499Ser", "hgvsWellDefined": "ENSP00000341551.3:p.Cys499Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS748110", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000342988.8:c.1495T>A" }, "RefSeq": { "hgvs": "NM_005359.6:c.1495T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000341551.3:p.Cys499Ser" }, "RefSeq": { "hgvs": "NP_005350.1:p.Cys499Ser" } } } }, { "coordinates": [ { "allele": "A", "end": 2033, "referenceAllele": "T", "start": 2032 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000342988.7:c.1495T>A" ], "proteinEffect": { "hgvs": "ENSP00000341551.3:p.Cys499Ser", "hgvsWellDefined": "ENSP00000341551.3:p.Cys499Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS261669" }, { "coordinates": [ { "allele": "A", "end": 1753, "referenceAllele": "T", "start": 1752 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000398417.6:c.1495T>A" ], "proteinEffect": { "hgvs": "ENSP00000381452.1:p.Cys499Ser", "hgvsWellDefined": "ENSP00000381452.1:p.Cys499Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS278258" }, { "coordinates": [ { "allele": "A", "end": 217, "referenceAllele": "T", "start": 216 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000586253.1:n.217T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS389268" }, { "coordinates": [ { "allele": "A", "end": 1207, "referenceAllele": "T", "start": 1206 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000588745.5:c.1207T>A" ], "proteinEffect": { "hgvs": "ENSP00000464901.1:p.Cys403Ser", "hgvsWellDefined": "ENSP00000464901.1:p.Cys403Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS390999" }, { "coordinates": [ { "allele": "A", "end": 3496, "referenceAllele": "T", "start": 3495 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000591126.5:n.3496T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS392668" }, { "coordinates": [ { "allele": "A", "end": 1142, "referenceAllele": "T", "start": 1141 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000592186.5:c.1142T>A" ], "proteinEffect": { "hgvs": "ENSP00000468611.1:n.1142T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS393389" }, { "coordinates": [ { "allele": "A", "end": 808, "referenceAllele": "T", "start": 807 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000611848.1:c.808T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS401041" }, { "@id": "http://reg.genome.network/allele/PA3085600265", "coordinates": [ { "allele": "A", "end": 2033, "referenceAllele": "T", "start": 2032 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "NM_005359.5:c.1495T>A", "LRG_318t1:c.1495T>A" ], "proteinEffect": { "hgvs": "NP_005350.1:p.Cys499Ser", "hgvsWellDefined": "NP_005350.1:p.Cys499Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS030461" }, { "@id": "http://reg.genome.network/allele/PA3085600265", "coordinates": [ { "allele": "A", "end": 2033, "referenceAllele": "T", "start": 2032 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "NM_005359.6:c.1495T>A" ], "proteinEffect": { "hgvs": "NP_005350.1:p.Cys499Ser", "hgvsWellDefined": "NP_005350.1:p.Cys499Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS696402", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000342988.8:c.1495T>A" }, "RefSeq": { "hgvs": "NM_005359.6:c.1495T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000341551.3:p.Cys499Ser" }, "RefSeq": { "hgvs": "NP_005350.1:p.Cys499Ser" } } } } ], "type": "nucleotide" }