ClinVar Miner

Submissions for variant NM_000038.5(APC):c.2952A>G (p.Glu984=) (rs772562489)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000571501 SCV000675900 likely benign Hereditary cancer-predisposing syndrome 2017-08-01 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Synonymous alterations with insufficient evidence to classify as benign
Color RCV000571501 SCV000681564 likely benign Hereditary cancer-predisposing syndrome 2017-01-09 criteria provided, single submitter clinical testing
GeneDx RCV000423032 SCV000522506 likely benign not specified 2015-12-24 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.
Integrated Genetics/Laboratory Corporation of America RCV000423032 SCV000918468 uncertain significance not specified 2017-12-11 criteria provided, single submitter clinical testing Variant summary: The APC c.2952A>G (p.Glu984Glu) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a damaging outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect binding of multiple ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 3/215300 control chromosomes (gnomAD) at a frequency of 0.0000139, which does not exceed the estimated maximal expected allele frequency of a pathogenic APC variant (0.0000714). One clinical diagnostic laboratory has classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. One internal sample (tested for inherited cancer panel) carrying this variant also carries CHEK2 c.444+1G>A. Taken together, this variant is classified as VUS-possibly benign.
Invitae RCV000543399 SCV000647285 likely benign Familial adenomatous polyposis 1 2017-04-25 criteria provided, single submitter clinical testing

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