ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1806C>G (p.Ala602=) (rs376046767)

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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 RCV000223290 SCV000278498 likely benign Hereditary cancer-predisposing syndrome 2015-09-15 criteria provided, single submitter clinical testing
Color RCV000223290 SCV000686164 likely benign Hereditary cancer-predisposing syndrome 2016-02-10 criteria provided, single submitter clinical testing
GeneDx RCV000434811 SCV000514207 benign not specified 2015-03-10 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 RCV000586194 SCV000697312 uncertain significance not provided 2016-11-17 criteria provided, single submitter clinical testing Variant summary: The PMS2 c.1806C>G (p.Ala602Ala) variant causes a synonymous change, which 5/5 splice prediction tools predict no significant impact on normal splicing and ESE finder predicts that this variant may affect binding of ESE site(s). However, these predictions have yet to be confirmed by functional studies. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 3/121342 (1/40485), which does not exceed the estimated maximal expected allele frequency for a pathogenic PMS2 variant of 1/8802. In addition, this observation needs to be cautiously considered due to the possibility of the pseudogene being captured, along with the cohort including individuals that may harbor a PMS2 phenotype. Two clinical diagnostic laboratories have classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as a "Variant of Uncertain Significance - Possibly Benign."
Invitae RCV000227868 SCV000285090 likely benign Hereditary nonpolyposis colon cancer 2017-11-16 criteria provided, single submitter clinical testing

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