ClinVar Miner

Submissions for variant NM_000249.3(MLH1):c.884+16A>G (rs377598055)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color RCV000579749 SCV000684878 likely benign Hereditary cancer-predisposing syndrome 2015-04-27 criteria provided, single submitter clinical testing
Counsyl RCV000411740 SCV000489196 likely benign Lynch syndrome II 2016-08-31 criteria provided, single submitter clinical testing
GeneDx RCV000160557 SCV000211135 benign not specified 2014-07-22 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.
Integrated Genetics/Laboratory Corporation of America RCV000589525 SCV000696186 uncertain significance not provided 2016-01-07 criteria provided, single submitter clinical testing Variant summary: This c.884+16A>G variant affects a non-conserved nucleotide, resulting in intronic change at a position not widely known to affect normal splicing. 4/5 splice-site tools via Alamut predict that this variant does not affect normal splicing. ESEfinder also predicts the variant not to affect any ESE binding sites. This variant was found in 22/121388 chromosomes from the broad and large populations of ExAC at a frequency of 0.0001812. It was mainly found in the European Non-Finnish sub-population where its allele frequency is 0.0003 (20/66728 chromosomes), which, albeit is lower than the maximal expected allele frequency in this gene (0.0007105), suggests that it might be a rare polymorphism in this population. To our knowledge, the variant has not been reported in affected individuals via publications and/or reputable databases/clinical laboratories; nor evaluated for functional impact by in vivo/vitro studies. One clinical lab has classified this variant as benign. Taken together, this variant has currently been classified as VUS-possibly benign.

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