ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1980C>T (p.Ala660=) (rs368928783)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163931 SCV000214527 likely benign Hereditary cancer-predisposing syndrome 2014-06-09 criteria provided, single submitter clinical testing
Color RCV000163931 SCV000691050 likely benign Hereditary cancer-predisposing syndrome 2017-08-24 criteria provided, single submitter clinical testing
GeneDx RCV000436373 SCV000518148 benign not specified 2015-08-05 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.
Illumina Clinical Services Laboratory,Illumina RCV000196833 SCV000469721 uncertain significance Lynch syndrome 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587189 SCV000697321 uncertain significance not provided 2016-10-21 criteria provided, single submitter clinical testing Variant summary: The c.1980C>T (p.Ala660=) in PMS2 gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the large control population dataset of ExAC at a low frequency 0.0000495 (6/121090 chrs tested), which does not exceed the estimated maximal expected allele frequency of a pathogenic PMS2 variant. However, some of these occurrences may due to a presence of a processed pseudogene, and, therefore, should be taken with cautions. The c.1980C>T has not, to our knowledge, been reported in affected individuals via published reports, but has been cited as Likely Benign by two reputable databases/clinical laboratories. Taken together, this variant has been classified as VUS-Possibly Benign.
Invitae RCV000524455 SCV000253293 likely benign Hereditary nonpolyposis colon cancer 2017-12-25 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000436373 SCV000601833 likely benign not specified 2016-10-04 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587189 SCV000889616 likely benign not provided 2018-04-06 criteria provided, single submitter clinical testing

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