ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.1662-10C>T (rs752606387)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000471574 SCV000559186 likely benign Hereditary nonpolyposis colon cancer 2018-01-05 criteria provided, single submitter clinical testing
Color RCV000580913 SCV000684960 likely benign Hereditary cancer-predisposing syndrome 2016-04-26 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590414 SCV000696221 uncertain significance not provided 2017-06-05 criteria provided, single submitter clinical testing Variant summary: The MSH2 c.1662-10C>T variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in ExAC and the literature in 33/118436 control chromosomes at a frequency of 0.0002786, which does not exceed the estimated maximal expected allele frequency of a pathogenic MSH2 variant (0.0005683). However, one publication reported that the variant is a common polymorphism in black South African controls (frequency = 0.34) suggesting the variant is benign (Davison_Dissertation_2012). In addition, one clinical diagnostic laboratory has classified this variant as likely benign. Taken together, this variant is classified as VUS-possibly benign.

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