ClinVar Miner

Submissions for variant NM_000038.5(APC):c.3650A>C (p.Asn1217Thr) (rs138933660)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000131570 SCV000186574 likely benign Hereditary cancer-predisposing syndrome 2018-02-22 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Internal frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance,In silico models in agreement (benign),Other data supporting benign classification
Color RCV000131570 SCV000911206 benign Hereditary cancer-predisposing syndrome 2016-03-21 criteria provided, single submitter clinical testing
Counsyl RCV000199645 SCV000488023 uncertain significance Familial adenomatous polyposis 1 2015-12-22 criteria provided, single submitter clinical testing
GeneDx RCV000120014 SCV000292457 likely benign not specified 2017-09-25 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.
ITMI RCV000120014 SCV000084144 not provided not specified 2013-09-19 no assertion provided reference population
Integrated Genetics/Laboratory Corporation of America RCV000587732 SCV000694035 likely benign not provided 2017-02-16 criteria provided, single submitter clinical testing Variant summary: The APC c.3650A>C (p.Asn1217Thr) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 28/120690 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.00254 (26/10238). This frequency is about 36 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 African origin. The variant was reported in the literature, without strong evidence for causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as uncertain significance while one has classified it as benign. Because of the relatively high frequency of the variant in the control population, this variant has been classified as likely benign.
Invitae RCV000199645 SCV000254010 benign Familial adenomatous polyposis 1 2017-10-31 criteria provided, single submitter clinical testing
PreventionGenetics RCV000587732 SCV000805401 uncertain significance not provided 2018-01-10 criteria provided, single submitter clinical testing

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