ClinVar Miner

Submissions for variant NM_000038.6(APC):c.2778T>C (p.Ser926=) (rs371526966)

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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 RCV000220698 SCV000275426 likely benign Hereditary cancer-predisposing syndrome 2015-04-23 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000507103 SCV000600063 likely benign not specified 2017-01-15 criteria provided, single submitter clinical testing
Invitae RCV000530592 SCV000647267 likely benign Familial adenomatous polyposis 1 2017-12-14 criteria provided, single submitter clinical testing
GeneDx RCV000507103 SCV000728926 likely benign not specified 2017-06-21 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 RCV000220698 SCV000904122 likely benign Hereditary cancer-predisposing syndrome 2018-02-05 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000507103 SCV000916508 likely benign not specified 2018-10-01 criteria provided, single submitter clinical testing Variant summary: APC c.2778T>C alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 2.9e-05 in 276802 control chromosomes and was observed exclusively in the African subpopulation of the gnomAD database at a frequency of 0.00033. This frequency is approximately 5-fold above the maximal expected allele frequency for a pathogenic variant in Familial Adenomatous Polyposis, suggesting the variant is a benign polymorphism found in populations of African ancestry. To our knowledge, no occurrence of c.2778T>C in individuals affected with Familial Adenomatous Polyposis and no experimental evidence demonstrating its impact on protein function have been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and all classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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