ClinVar Miner

Submissions for variant NM_000251.3(MSH2):c.2458+10A>G

dbSNP: rs1269379998
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000583562 SCV000690071 likely benign Hereditary cancer-predisposing syndrome 2016-02-17 criteria provided, single submitter clinical testing
GeneDx RCV000604544 SCV000732748 likely benign not specified 2017-06-26 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 RCV000898368 SCV001042574 likely benign Hereditary nonpolyposis colorectal neoplasms 2024-01-19 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000604544 SCV001362998 uncertain significance not specified 2019-04-01 criteria provided, single submitter clinical testing Variant summary: MSH2 c.2458+10A>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing at the canonical splice site. One computational tool predicts the creation of a cryptic intronic 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 276928 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.2458+10A>G in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as VUS-possibly benign.
Genetic Services Laboratory, University of Chicago RCV000604544 SCV002067815 uncertain significance not specified 2019-11-25 criteria provided, single submitter clinical testing

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