ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1209C>T (p.Ser403=) (rs147399413)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000166110 SCV000216878 likely benign Hereditary cancer-predisposing syndrome 2014-10-02 criteria provided, single submitter clinical testing
GeneDx RCV000422391 SCV000514200 benign not specified 2015-05-05 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.
Invitae RCV001088731 SCV000562236 likely benign Hereditary nonpolyposis colorectal neoplasms 2019-12-31 criteria provided, single submitter clinical testing
Color RCV000166110 SCV000686107 likely benign Hereditary cancer-predisposing syndrome 2017-01-03 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587597 SCV000697284 benign not provided 2017-06-16 criteria provided, single submitter clinical testing Variant summary: The c.1209C>T (p.Ser403=) in PMS2 gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant do not affect a normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in control population dataset of ExAC at a frequency of 9.257e-05 (11/118826 chrs tested), predominantly in individuals of Latino descent (0.0008666; 10/11540 chrs tested). The later frequency exceeds the estimated maximal expected allele frequency of a pathogenic variant in PMS2 gene (0.00011). The variant was cited as Likely Benign/Benign by a reputable database/clinical laboratories. Taking together, the variant was classified as Benign.
PreventionGenetics,PreventionGenetics RCV000587597 SCV000806166 likely benign not provided 2017-10-23 criteria provided, single submitter clinical testing

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