ClinVar Miner

Submissions for variant NM_000038.6(APC):c.5268T>A (p.Ser1756=) (rs866006)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000166360 SCV000217149 likely benign Hereditary cancer-predisposing syndrome 2014-11-18 criteria provided, single submitter clinical testing
GeneDx RCV000424383 SCV000512077 benign not specified 2015-07-20 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.
Invitae RCV001081989 SCV000562652 likely benign Familial adenomatous polyposis 1 2019-12-31 criteria provided, single submitter clinical testing
Color RCV000166360 SCV000681722 likely benign Hereditary cancer-predisposing syndrome 2016-11-22 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000758733 SCV000887534 benign not provided 2017-12-04 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001151700 SCV001312865 benign APC-Associated Polyposis Disorders 2017-09-07 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Integrated Genetics/Laboratory Corporation of America RCV000424383 SCV001362434 benign not specified 2019-01-18 criteria provided, single submitter clinical testing Variant summary: APC c.5268T>A 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 7.3e-05 in 245272 control chromosomes. The observed variant frequency is approximately equal to 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 benign. c.5268T>A has been reported in the literature in individuals (Zhou_2004). These report(s) do not provide unequivocal conclusions about association of the variant with Familial Adenomatous Polyposis. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four 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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