ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.2187C>G (p.Leu729=) (rs373630535)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000162439 SCV000212788 likely benign Hereditary cancer-predisposing syndrome 2014-06-20 criteria provided, single submitter clinical testing
Counsyl RCV000662897 SCV000785817 likely benign Hereditary nonpolyposis colorectal cancer type 4 2017-12-11 criteria provided, single submitter clinical testing
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia RCV000197459 SCV000257703 likely benign Lynch syndrome 2015-03-06 criteria provided, single submitter clinical testing
GeneDx RCV000127465 SCV000171037 benign not specified 2013-12-31 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.
Genetic Services Laboratory, University of Chicago RCV000127465 SCV000596466 likely benign not specified 2016-06-22 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590780 SCV000697340 benign not provided 2016-02-15 criteria provided, single submitter clinical testing Variant summary: The c.2187C>G variant affects a non-conserved nucleotide, resulting in no amino acid change. 5/5 programs in Alamut predict that this variant does not affect normal splicing. ESE finder predicts that this variant may affect multiple ESE sites. However, these predictions are not confirmed by experimental studies. This variant is found in 106/81156 control chromosomes (5 homozygotes) at a frequency of 0.0013061, which is about 11 times of maximal expected frequency of a pathogenic allele (0.0001136). Even considering the possibility that these occurrences may be from a PMS2 pseudogene, 5 homozygotes found in controls suggest this variant is benign. In addition, multiple clinical laboratories classified this variant as benign/likely benign. The variant of interest has not been evaluated for functional impact by in vivo/in vitro studies. Taken together, this variant was classified as benign.
Invitae RCV000197459 SCV000252715 benign Lynch syndrome 2016-03-20 criteria provided, single submitter clinical testing
PreventionGenetics RCV000127465 SCV000806201 benign not specified 2017-02-24 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000127465 SCV000601840 likely benign not specified 2017-03-13 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000590780 SCV000888401 benign not provided 2018-03-15 criteria provided, single submitter clinical testing

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