ClinVar Miner

Submissions for variant NM_000038.6(APC):c.5027G>C (p.Arg1676Thr)

gnomAD frequency: 0.00025  dbSNP: rs143674116
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000130120 SCV000184952 likely benign Hereditary cancer-predisposing syndrome 2019-01-28 criteria provided, single submitter clinical testing In silico models in agreement (benign);Internal frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance;Subpopulation frequency in support of benign classification
GeneDx RCV000589678 SCV000292990 likely benign not provided 2021-05-13 criteria provided, single submitter clinical testing
Invitae RCV002228484 SCV000552750 likely benign Familial adenomatous polyposis 1 2021-12-02 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000722124 SCV000694068 benign not specified 2022-02-10 criteria provided, single submitter clinical testing Variant summary: APC c.5027G>C (p.Arg1676Thr) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 7.2e-05 in 250184 control chromosomes, predominantly at a frequency of 0.0011 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 15.4 fold of 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 a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.5027G>C in individuals affected with Familial Adenomatous Polyposis and no experimental evidence demonstrating its impact on protein function have been reported. Five ClinVar submitters have assessed the variant since 2014: four classified the variant as likely benign and one as benign. Based on the evidence outlined above, the variant was classified as benign.
Color Health, Inc RCV000130120 SCV000902908 likely benign Hereditary cancer-predisposing syndrome 2016-03-18 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000722124 SCV001469311 benign not specified 2020-08-18 criteria provided, single submitter clinical testing

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