ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.3556+36_3556+39del (rs55684722)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000409782 SCV000489197 likely benign Hereditary nonpolyposis colorectal cancer type 5 2016-08-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588085 SCV000695873 benign not provided 2017-04-20 criteria provided, single submitter clinical testing Variant summary: The MSH6 c.3556+36_3556+39delGTCA variant involves the deletion of 4 intronic nucleotides. One in silico tool predicts a benign outcome for this variant. 2/5 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 18/120584 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.001646 (17/10328). This frequency is about 12 times the estimated maximal expected allele frequency of a pathogenic MSH6 variant (0.0001421), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, one clinical diagnostic laboratory/reputable database has classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.

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