ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.1276+16G>A (rs368120695)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000411558 SCV000489665 likely benign Lynch syndrome I 2016-11-02 criteria provided, single submitter clinical testing
GeneDx RCV000421899 SCV000513658 benign not specified 2015-08-17 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.
Color Health, Inc RCV000579646 SCV000684921 likely benign Hereditary cancer-predisposing syndrome 2016-05-10 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000587782 SCV000696205 uncertain significance not provided 2016-12-01 criteria provided, single submitter clinical testing Variant summary: The MSH2 c.1276+16G>A variant involves the alteration of a non-conserved intronic nucleotide. Mutation Taster predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESEfinder also predicts no effect in binding sites for ESEs. However, these predictions have yet to be confirmed by functional studies. This variant was found in 2/117144 control chromosomes from ExAC at a frequency of 0.0000171, which does not exceed the estimated maximal expected allele frequency of a pathogenic MSH2 variant (0.0005683). The variant was only found in African subpopulation. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories, nor evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a variant of uncertain significance (VUS) until additional information becomes available.

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