ClinVar Miner

Submissions for variant NM_000038.6(APC):c.2640C>T (p.Ile880=) (rs200184105)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001083352 SCV000166024 benign Familial adenomatous polyposis 1 2020-11-18 criteria provided, single submitter clinical testing
GeneDx RCV000432457 SCV000515417 likely benign not specified 2017-12-07 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.
Ambry Genetics RCV000491406 SCV000579819 likely benign Hereditary cancer-predisposing syndrome 2015-02-13 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000432457 SCV000600061 benign not specified 2019-11-22 criteria provided, single submitter clinical testing
Color Health, Inc RCV000491406 SCV000681545 likely benign Hereditary cancer-predisposing syndrome 2016-10-02 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589008 SCV000694016 likely benign not provided 2016-11-18 criteria provided, single submitter clinical testing Variant summary: The APC c.2640C>T (p.Ile880Ile) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 4/121320 control chromosomes, predominantly observed in the Latino subpopulation at a frequency of 0.0002594 (3/11566). This frequency is about 4 times the estimated maximal expected allele frequency of a pathogenic APC variant (0.0000714), suggesting this is likely a benign polymorphism found primarily in the populations of Latino origin. In addition, 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. Taken together, this variant is classified as likely benign.

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