ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.260+7G>A (rs774479750)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000438252 SCV000516714 likely benign not specified 2016-12-15 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.
Invitae RCV001081272 SCV000561480 likely benign Hereditary nonpolyposis colorectal neoplasms 2019-12-31 criteria provided, single submitter clinical testing
Color RCV000582801 SCV000690279 likely benign Hereditary cancer-predisposing syndrome 2017-06-13 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000679227 SCV000805869 likely benign not provided 2016-12-30 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000679227 SCV000888262 likely benign not provided 2017-09-20 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000438252 SCV001360646 uncertain significance not specified 2019-11-29 criteria provided, single submitter clinical testing Variant summary: MSH6 c.260+7G>A alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: One predict the variant weakens a cryptic 5 donor site. Two predict the variant creates a cryptic 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4.6e-05 in 43282 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.260+7G>A in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Five ClinVar submissions (evaluation after 2014) cites the variant as likely benign. Based on the evidence outlined above, the variant was classified as VUS - possibly benign.

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