ClinVar Miner

Submissions for variant NM_000038.6(APC):c.2262T>G (p.Val754=) (rs148987776)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000122761 SCV000166018 benign Familial adenomatous polyposis 1 2018-01-09 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000152789 SCV000202177 likely benign not specified 2014-04-30 criteria provided, single submitter clinical testing
Ambry Genetics RCV000163307 SCV000213835 likely benign Hereditary cancer-predisposing syndrome 2014-10-09 criteria provided, single submitter clinical testing
Counsyl RCV000122761 SCV000487788 likely benign Familial adenomatous polyposis 1 2015-11-17 criteria provided, single submitter clinical testing
GeneDx RCV000152789 SCV000512069 benign not specified 2015-03-27 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 RCV000163307 SCV000681512 benign Hereditary cancer-predisposing syndrome 2016-03-18 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000152789 SCV000805378 benign not specified 2017-01-10 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000758722 SCV000887509 benign not provided 2017-08-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000152789 SCV000918464 benign not specified 2017-12-04 criteria provided, single submitter clinical testing Variant summary: The APC c.2262T>G (p.Val754Val) variant involves the alteration of a non-conserved nucleotide causing a synonymous change and 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may create ESE binding sites at the locus. However, these predictions have yet to be confirmed by functional studies. This variant was found in 102/276142 control chromosomes (gnomAD), predominantly observed in the African subpopulation at a frequency of 0.003833 (92/24002). This frequency is about 54 times the estimated maximal expected allele frequency of a pathogenic APC variant (0.0000714), strongly suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign or benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as benign.

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