ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1587G>A (p.Ser529=) (rs786201709)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000164137 SCV000214753 likely benign Hereditary cancer-predisposing syndrome 2016-09-22 criteria provided, single submitter clinical testing
Color RCV000164137 SCV000686143 likely benign Hereditary cancer-predisposing syndrome 2016-12-12 criteria provided, single submitter clinical testing
GeneDx RCV000427627 SCV000525306 likely benign not specified 2017-08-17 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 RCV000427627 SCV000920050 uncertain significance not specified 2018-08-17 criteria provided, single submitter clinical testing Variant summary: PMS2 c.1587G>A alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 245570 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.1587G>A in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submissions from other clinical diagnostic laboratories (evaluation after 2014) cite the variant as "likely benign." Based on the evidence outlined above, the variant was classified as VUS-possibly benign.
Invitae RCV000230403 SCV000285077 likely benign Lynch syndrome 2016-03-18 criteria provided, single submitter clinical testing

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