ClinVar Miner

Submissions for variant NM_000251.2(MSH2):c.1510+1G>A (rs1114167852)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000491735 SCV000580558 likely pathogenic Hereditary cancer-predisposing syndrome 2014-06-18 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000780446 SCV000917699 likely pathogenic Lynch syndrome 2018-04-30 criteria provided, single submitter clinical testing Variant summary: MSH2 c.1510+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Five predict the variant abolishes a 5 splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was observed with an allele frequency of 4.1e-06 in 246122 control chromosomes (gnomAD). The variant, c.1510+1G>A, has been reported in the literature as a pathogenic/likely pathogenic variant reported by a clinical diagnostic laboratory with limited information (LaDuca_2017). These report(s) do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. In 2014, one clinical diagnostic laboratory reporting the single published occurrence of this variant submitted clinical-significance assessment for this variant as "Likely Pathogenic" in ClinVar. Based on the evidence outlined above, the variant was classified as Likely Pathogenic.

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