ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1560G>A (p.Ala520=) (rs201167814)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000162432 SCV000212779 likely benign Hereditary cancer-predisposing syndrome 2014-05-23 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000487654 SCV000575509 uncertain significance not provided 2016-09-30 criteria provided, single submitter clinical testing
Color RCV000162432 SCV000537477 likely benign Hereditary cancer-predisposing syndrome 2015-06-15 criteria provided, single submitter clinical testing
GeneDx RCV000127461 SCV000171028 benign not specified 2014-01-22 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 RCV000487654 SCV000697302 benign not provided 2017-06-26 criteria provided, single submitter clinical testing Variant summary: The c.1560G>A (p.Ala520=) in PMS2 gene is a synonymous change that involves a non-conserved nucleotide. 4/5 programs in Alamut predict that this variant does not affect the normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population datasets of ExAC and gnomAD at a similar frequencies 0.00033 (38/120402 and 93/277018 chrs tested, respectively), which is about 3 times of the maximum expected allele frequency for a pathogenic PMS2 variant (0.00011). Sequence allignment and reads in ExAC support that the minor alleles reported in ExAC are not from the pseudogene. The variant has not, to our knowledge, been reported in affected individuals via published reports but is cited as Benign/Likely Benign by reputable databases/clinical laboratories. Taking together, the variant was classified as benign.
Invitae RCV000199295 SCV000253288 likely benign Hereditary nonpolyposis colon cancer 2017-12-24 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000127461 SCV000601823 likely benign not specified 2016-10-14 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000487654 SCV000888395 likely benign not provided 2017-12-04 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000162432 SCV000788106 likely benign Hereditary cancer-predisposing syndrome 2017-09-27 no assertion criteria provided clinical testing

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