ClinVar Miner

Submissions for variant NM_000038.6(APC):c.388A>G (p.Ser130Gly) (rs150973053)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000122775 SCV000166032 benign Familial adenomatous polyposis 1 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000129715 SCV000184518 likely benign Hereditary cancer-predisposing syndrome 2018-07-16 criteria provided, single submitter clinical testing Subpopulation frequency in support of benign classification;Other data supporting benign classification
GeneDx RCV000211891 SCV000209564 likely benign not specified 2017-10-23 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.
Integrated Genetics/Laboratory Corporation of America RCV000211891 SCV000694040 likely benign not specified 2019-10-10 criteria provided, single submitter clinical testing Variant summary: APC c.388A>G (p.Ser130Gly) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00035 in 253354 control chromosomes. The observed variant frequency is approximately 5 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 benign. c.388A>G has been reported in the literature in individuals affected with Familial Adenomatous Polyposis, HBOC or colorectal cancer (Maxwell_2016, Cleary_2008, Rosa_2004, Rey_2017). These reports do not provide unequivocal conclusions about association of the variant with Familial Adenomatous Polyposis. Co-occurrence with a pathogenic variant has been reported (APC c.3815C>G, p.Ser1272X), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six other ClinVar submitters (evaluation after 2014) cite the variant as likely benign/benign (x5) or VUS (x1). Based on the evidence outlined above, the variant was classified as likely benign.
Mendelics RCV000122775 SCV000838062 likely benign Familial adenomatous polyposis 1 2018-07-02 criteria provided, single submitter clinical testing
Color RCV000129715 SCV000902599 likely benign Hereditary cancer-predisposing syndrome 2016-03-18 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000034387 SCV001133330 benign not provided 2019-02-13 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001155264 SCV001316683 uncertain significance APC-Associated Polyposis Disorders 2018-01-26 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000034387 SCV001371504 likely benign not provided 2020-04-01 criteria provided, single submitter clinical testing
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034387 SCV000043104 variant of unknown significance not provided 2012-07-13 no assertion criteria provided research Converted during submission to Uncertain significance.
CSER _CC_NCGL, University of Washington RCV000417265 SCV000503532 uncertain significance Familial adenomatous polyposis 2016-08-01 no assertion criteria provided research Found in patient having exome sequencing due to suspicion for hereditary colon cancer and/or polyps. Patient is a 40 year old with a history of colon cancer diagnosed at age 39 and a family history of colon polyps.

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