ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.2109G>A (p.Thr703=) (rs775355718)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000166236 SCV000217016 likely benign Hereditary cancer-predisposing syndrome 2014-10-03 criteria provided, single submitter clinical testing
GeneDx RCV000422475 SCV000528185 likely benign not specified 2016-05-23 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 RCV000422475 SCV000920031 uncertain significance not specified 2017-11-03 criteria provided, single submitter clinical testing Variant summary: The PMS2 c.2109G>A (p.Thr703Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 5/251270 control chromosomes at a frequency of 0.0000199, which does not exceed the estimated maximal expected allele frequency of a pathogenic PMS2 variant (0.0001136). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as VUS-possibly benign.

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