{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA402465098", "communityStandardTitle": [ "NM_005359.6(SMAD4):c.1309G>A (p.Val437Ile)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=618917[alleleid]", "alleleId": 618917, "preferredName": "NM_005359.6(SMAD4):c.1309G>A (p.Val437Ile)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/630855", "RCV": [ "RCV000776864", "RCV001262036", "RCV001856136" ], "variationId": 630855 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr18:g.48603008G>A?assembly=hg19", "id": "chr18:g.48603008G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr18:g.51076638G>A?assembly=hg38", "id": "chr18:g.51076638G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1568211172", "rs": 1568211172 } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/18-51076638-G-A?dataset=gnomad_r4", "id": "18-51076638-G-A", "variant": "18:51076638 G / A" } ] }, "genomicAlleles": [ { "chromosome": "18", "coordinates": [ { "allele": "A", "end": 51076638, "referenceAllele": "G", "start": 51076637 } ], "hgvs": [ "NC_000018.10:g.51076638G>A", "CM000680.2:g.51076638G>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000066" }, { "chromosome": "18", "coordinates": [ { "allele": "A", "end": 48603008, "referenceAllele": "G", "start": 48603007 } ], "hgvs": [ "NC_000018.9:g.48603008G>A", "CM000680.1:g.48603008G>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000042" }, { "chromosome": "18", "coordinates": [ { "allele": "A", "end": 46857006, "referenceAllele": "G", "start": 46857005 } ], "hgvs": [ "NC_000018.8:g.46857006G>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000018" }, { "coordinates": [ { "allele": "A", "end": 113599, "referenceAllele": "G", "start": 113598 } ], "hgvs": [ "NG_013013.2:g.113599G>A", "LRG_318:g.113599G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS002660" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1574, "referenceAllele": "G", "start": 1573 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000588860.6:c.1309G>A" ], "proteinEffect": { "hgvs": "ENSP00000465878.2:p.Val437Ile", "hgvsWellDefined": "ENSP00000465878.2:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS914337" }, { "coordinates": [ { "allele": "A", "end": 1613, "referenceAllele": "G", "start": 1612 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000589076.6:c.1309G>A" ], "proteinEffect": { "hgvs": "ENSP00000466934.2:p.Val437Ile", "hgvsWellDefined": "ENSP00000466934.2:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS914338" }, { "coordinates": [ { "allele": "A", "end": 2016, "referenceAllele": "G", "start": 2015 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000589941.2:c.1309G>A" ], "proteinEffect": { "hgvs": "ENSP00000465874.2:p.Val437Ile", "hgvsWellDefined": "ENSP00000465874.2:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS914340" }, { "coordinates": [ { "allele": "A", "end": 1432, "referenceAllele": "G", "start": 1431 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000590061.2:c.1309G>A" ], "proteinEffect": { "hgvs": "ENSP00000464772.2:p.Val437Ile", "hgvsWellDefined": "ENSP00000464772.2:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS914342" }, { "coordinates": [ { "allele": "A", "end": 1841, "referenceAllele": "G", "start": 1840 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000593223.2:c.1309G>A" ], "proteinEffect": { "hgvs": "ENSP00000466118.2:p.Val437Ile", "hgvsWellDefined": "ENSP00000466118.2:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS914349" }, { "coordinates": [ { "allele": "A", "end": 1436, "referenceAllele": "G", "start": 1435 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000611848.2:c.1309G>A" ], "proteinEffect": { "hgvs": "ENSP00000478613.2:p.Val437Ile", "hgvsWellDefined": "ENSP00000478613.2:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS826412" }, { "coordinates": [ { "allele": "A", "end": 2681, "referenceAllele": "G", "start": 2680 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000684953.1:n.2681G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS829809" }, { "coordinates": [ { "allele": "A", "end": 1760, "referenceAllele": "G", "start": 1759 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000685090.1:n.1760G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS829875" }, { "coordinates": [ { "allele": "A", "end": 1417, "referenceAllele": "G", "start": 1416 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000685232.1:n.1417G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS829955" }, { "coordinates": [ { "allele": "A", "end": 1417, "referenceAllele": "G", "start": 1416 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000688574.1:n.1417G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS831698" }, { "coordinates": [ { "allele": "A", "end": 2791, "referenceAllele": "G", "start": 2790 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000691124.1:n.2791G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS833056" }, { "coordinates": [ { "allele": "A", "end": 1847, "referenceAllele": "G", "start": 1846 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000342988.8:c.1309G>A" ], "proteinEffect": { "hgvs": "ENSP00000341551.3:p.Val437Ile", "hgvsWellDefined": "ENSP00000341551.3:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS748110", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000342988.8:c.1309G>A" }, "RefSeq": { "hgvs": "NM_005359.6:c.1309G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000341551.3:p.Val437Ile" }, "RefSeq": { "hgvs": "NP_005350.1:p.Val437Ile" } } } }, { "coordinates": [ { "allele": "A", "end": 1847, "referenceAllele": "G", "start": 1846 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000342988.7:c.1309G>A" ], "proteinEffect": { "hgvs": "ENSP00000341551.3:p.Val437Ile", "hgvsWellDefined": "ENSP00000341551.3:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS261669" }, { "coordinates": [ { "allele": "A", "end": 1567, "referenceAllele": "G", "start": 1566 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000398417.6:c.1309G>A" ], "proteinEffect": { "hgvs": "ENSP00000381452.1:p.Val437Ile", "hgvsWellDefined": "ENSP00000381452.1:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS278258" }, { "coordinates": [ { "allele": "A", "end": 1021, "referenceAllele": "G", "start": 1020 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000588745.5:c.1021G>A" ], "proteinEffect": { "hgvs": "ENSP00000464901.1:p.Val341Ile", "hgvsWellDefined": "ENSP00000464901.1:p.Val341Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS390999" }, { "coordinates": [ { "allele": "A", "end": 367, "referenceAllele": "G", "start": 366 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000590499.1:n.367G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS392231" }, { "coordinates": [ { "allele": "A", "end": 3310, "referenceAllele": "G", "start": 3309 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000591126.5:n.3310G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS392668" }, { "coordinates": [ { "allele": "A", "end": 956, "referenceAllele": "G", "start": 955 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000592186.5:c.956G>A" ], "proteinEffect": { "hgvs": "ENSP00000468611.1:p.Gly319Asp", "hgvsWellDefined": "ENSP00000468611.1:p.Gly319Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS393389" }, { "coordinates": [ { "allele": "A", "end": 76, "referenceAllele": "G", "start": 75 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000593223.1:c.76G>A" ], "proteinEffect": { "hgvs": "ENSP00000466118.1:p.Val26Ile", "hgvsWellDefined": "ENSP00000466118.1:p.Val26Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS394097" }, { "coordinates": [ { "allele": "A", "end": 509, "referenceAllele": "G", "start": 508 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "ENST00000611848.1:c.509G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS401041" }, { "@id": "http://reg.genome.network/allele/PA913197150", "coordinates": [ { "allele": "A", "end": 1847, "referenceAllele": "G", "start": 1846 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "NM_005359.5:c.1309G>A", "LRG_318t1:c.1309G>A" ], "proteinEffect": { "hgvs": "NP_005350.1:p.Val437Ile", "hgvsWellDefined": "NP_005350.1:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS030461" }, { "@id": "http://reg.genome.network/allele/PA913197150", "coordinates": [ { "allele": "A", "end": 1847, "referenceAllele": "G", "start": 1846 } ], "gene": "http://reg.genome.network/gene/GN006770", "geneNCBI_id": 4089, "geneSymbol": "SMAD4", "hgvs": [ "NM_005359.6:c.1309G>A" ], "proteinEffect": { "hgvs": "NP_005350.1:p.Val437Ile", "hgvsWellDefined": "NP_005350.1:p.Val437Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS696402", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000342988.8:c.1309G>A" }, "RefSeq": { "hgvs": "NM_005359.6:c.1309G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000341551.3:p.Val437Ile" }, "RefSeq": { "hgvs": "NP_005350.1:p.Val437Ile" } } } } ], "type": "nucleotide" }