ClinVar Miner

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

gnomAD frequency: 0.00096  dbSNP: rs148987776
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002228416 SCV000166018 benign Familial adenomatous polyposis 1 2021-12-17 criteria provided, single submitter clinical testing
Eurofins NTD LLC (GA) 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 This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
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 Diagnostics, LLC DBA Color Health 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
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 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.
Genetic Services Laboratory,University of Chicago RCV000152789 SCV002066398 likely benign not specified 2019-02-14 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000163307 SCV002529051 benign Hereditary cancer-predisposing syndrome 2020-10-01 criteria provided, single submitter curation

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