ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.379G>A (p.Ala127Thr) (rs114090343)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000121857 SCV000171046 benign not specified 2014-06-02 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.
Ambry Genetics RCV000129112 SCV000183825 likely benign Hereditary cancer-predisposing syndrome 2018-11-09 criteria provided, single submitter clinical testing Subpopulation frequency in support of benign classification;In silico models in agreement (benign)
Invitae RCV001084398 SCV000218861 benign Hereditary nonpolyposis colon cancer 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001095167 SCV000469740 likely benign Hereditary nonpolyposis colorectal cancer type 4 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Genetic Services Laboratory, University of Chicago RCV000121857 SCV000596472 likely benign not specified 2016-05-25 criteria provided, single submitter clinical testing
Color RCV000129112 SCV000686198 likely benign Hereditary cancer-predisposing syndrome 2015-04-28 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590269 SCV000697366 likely benign not provided 2017-05-15 criteria provided, single submitter clinical testing
University of Washington Department of Laboratory Medicine, University of Washington RCV000168196 SCV000887462 uncertain significance Lynch syndrome 2018-05-01 criteria provided, single submitter clinical testing PMS2 NM_000535.5:c.379G>A has a 70.8% probability of pathogenicity based on combining prior probability from public data with likelihood ratios of 1.56 and 1.56 to 1, generated from evidence of seeing this as a somatic mutation in two independent tumors without loss of heterozygosity at the PMS2 locus. See Shirts et al 2018, PMID 29887214.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000590269 SCV000889626 benign not provided 2017-12-29 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000121857 SCV001160411 likely benign not specified 2019-03-27 criteria provided, single submitter clinical testing
ITMI RCV000121857 SCV000086059 not provided not specified 2013-09-19 no assertion provided reference population
Ding PR Lab,Sun Yat-sen University Cancer Center RCV001093698 SCV001250882 uncertain significance Lynch syndrome I no assertion criteria provided clinical testing

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