ClinVar Miner

Submissions for variant NM_000038.6(APC):c.5506G>A (p.Gly1836Arg) (rs766739164)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001087232 SCV000282781 likely benign Familial adenomatous polyposis 1 2020-12-04 criteria provided, single submitter clinical testing
GeneDx RCV000478919 SCV000569766 uncertain significance not provided 2020-02-13 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV000561275 SCV000667290 likely benign Hereditary cancer-predisposing syndrome 2018-06-20 criteria provided, single submitter clinical testing Other data supporting benign classification;Subpopulation frequency in support of benign classification
PreventionGenetics,PreventionGenetics RCV000478919 SCV000805435 uncertain significance not provided 2017-01-10 criteria provided, single submitter clinical testing
Color Health, Inc RCV000561275 SCV000902919 benign Hereditary cancer-predisposing syndrome 2017-02-10 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000478919 SCV001133349 benign not provided 2019-02-05 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001192984 SCV001361482 likely benign not specified 2021-05-10 criteria provided, single submitter clinical testing Variant summary: APC c.5506G>A (p.Gly1836Arg) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00019 in 250906 control chromosomes, predominantly at a frequency of 0.0013 within the Latino subpopulation in the gnomAD database. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 18-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 Latino origin. To our knowledge, no occurrence of c.5506G>A in individuals affected with Familial Adenomatous Polyposis and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submitters (evaluation after 2014) cite the variant as benign/likely benign and two ClinVar submitters (evaluation after 2014) cite it as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.

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