ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3739G>A (p.Ala1247Thr) (rs148223181)

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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 RCV000163815 SCV000214399 benign Hereditary cancer-predisposing syndrome 2015-05-14 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Co-occurence with a mutation in another gene that clearly explains a proband's phenotype,Other strong data supporting benign classification,In silico models in agreement (benign)
Invitae RCV000589358 SCV000259947 benign not provided 2019-02-27 criteria provided, single submitter clinical testing
GeneDx RCV000235835 SCV000293067 likely benign not specified 2017-08-31 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 RCV000589358 SCV000694036 likely benign not provided 2017-07-06 criteria provided, single submitter clinical testing Variant summary: The APC c.3739G>A (p.Ala1247Thr) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 12/122350 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.001086 (11/10130). This frequency is about 15 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. This variant has been reported in a CRC patient without strong evidence for causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign and one other lab classified it as VUS, all without evidence for independent evaluation. Taken together, this variant is classified as likely benign.
Color RCV000163815 SCV000910767 benign Hereditary cancer-predisposing syndrome 2016-03-23 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589358 SCV001133327 benign not provided 2018-10-11 criteria provided, single submitter clinical testing

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