ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3963C>T (p.Ser1321=) (rs150595875)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163353 SCV000213887 likely benign Hereditary cancer-predisposing syndrome 2014-11-18 criteria provided, single submitter clinical testing
Invitae RCV000198063 SCV000252586 benign Familial adenomatous polyposis 1 2017-10-23 criteria provided, single submitter clinical testing
GeneDx RCV000441140 SCV000512074 benign not specified 2015-07-27 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Color RCV000163353 SCV000681644 likely benign Hereditary cancer-predisposing syndrome 2016-04-19 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759428 SCV000888741 benign not provided 2018-01-15 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000441140 SCV000916507 benign not specified 2018-09-28 criteria provided, single submitter clinical testing Variant summary: APC c.3963C>T alters a non-conserved nucleotide resulting in a synonymous change. The variant allele was found at a frequency of 0.00015 in 276872 control chromosomes, predominantly at a frequency of 0.0017 within the African subpopulation in the gnomAD database. The observed variant frequency within African control individuals in the gnomAD database is approximately 23.8 fold of the estimated maximal expected allele frequency for a pathogenic variant in APC causing Familial Adenomatous Polyposis phenotype (7.1e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.3963C>T in individuals affected with Familial Adenomatous Polyposis and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

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