ClinVar Miner

Submissions for variant NM_000038.6(APC):c.5140G>A (p.Asp1714Asn) (rs148275069)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000587086 SCV000166041 likely benign not provided 2019-03-04 criteria provided, single submitter clinical testing
Ambry Genetics RCV000129088 SCV000183796 likely benign Hereditary cancer-predisposing syndrome 2017-07-20 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: In silico models in agreement (benign),Other data supporting benign classification
GeneDx RCV000479916 SCV000564574 likely benign not specified 2017-11-22 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587086 SCV000600110 likely benign not provided 2019-08-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587086 SCV000694069 likely benign not provided 2016-12-05 criteria provided, single submitter clinical testing Variant summary: The APC c.5140G>A (p.Asp1714Asn) variant causes a missense change involving a conserved nucleotide, which 2/4 in silico tools (SNPs&GO not captured due to low reliability index) predict a benign outcome, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 24/122192 (1/5010), which does exceed the maximal expected allele frequency for a pathogenic APC variant of 1/14005. Multiple publications cite the variant in affected individuals, while multiple clinical diagnostic laboratories cite the variant with conflicting classifications "uncertain significance" or "likely benign." Therefore, due to the high prevalence in the control cohort, the variant of interest has been classified as likely benign.
PreventionGenetics,PreventionGenetics RCV000587086 SCV000805422 uncertain significance not provided 2014-03-11 criteria provided, single submitter clinical testing
Mendelics RCV000122784 SCV000838131 uncertain significance Familial adenomatous polyposis 1 2018-07-02 criteria provided, single submitter clinical testing
Color RCV000129088 SCV000910666 likely benign Hereditary cancer-predisposing syndrome 2016-11-22 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000587086 SCV001154471 uncertain significance not provided 2017-02-01 criteria provided, single submitter clinical testing
CSER _CC_NCGL, University of Washington RCV000122784 SCV000190065 uncertain significance Familial adenomatous polyposis 1 2014-06-01 no assertion criteria provided research

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