ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1320A>G (p.Pro440=)

gnomAD frequency: 0.00012  dbSNP: rs138697590
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001082973 SCV000166369 likely benign Hereditary nonpolyposis colorectal neoplasms 2021-12-17 criteria provided, single submitter clinical testing
GeneDx RCV000127460 SCV000171025 benign not specified 2014-03-18 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 RCV000162674 SCV000213121 likely benign Hereditary cancer-predisposing syndrome 2014-09-17 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Color Diagnostics, LLC DBA Color Health RCV000162674 SCV000537450 likely benign Hereditary cancer-predisposing syndrome 2015-04-27 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000127460 SCV000601814 likely benign not specified 2017-06-23 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000127460 SCV000697293 benign not specified 2020-09-17 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588011 SCV000888389 likely benign not provided 2017-06-23 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000588011 SCV002049328 likely benign not provided 2020-10-09 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000127460 SCV002066516 likely benign not specified 2021-10-11 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000162674 SCV002529783 likely benign Hereditary cancer-predisposing syndrome 2021-08-04 criteria provided, single submitter curation
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001356109 SCV001551181 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The PMS2 p.Pro440= variant was not identified in the literature nor was it identified in the COGR, Cosmic, MutDB, LOVD 3.0, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors Database. The variant was identified in dbSNP (ID: rs138697590) “With Likely benign allele”, ClinVar (classified with conflicting interpretations of pathogenicity: likely benign by Invitae, Ambry Genetics, Color Genomics Inc, Quest Diagnostics Nichols Institute San Juan Capistrano; benign by GeneDx, and uncertain significance by Laboratory Corporation of America), Clinvitae (3x), and in control databases in 20 of 277136 chromosomes at a frequency of 0.00007, increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 2 of 24024 chromosomes (freq: 0.00008) and European Non-Finnish in 18 of 126664 chromosomes (freq: 0.0001) but not in the Other, Latino, Ashkenazi Jewish, East Asian, European Finnish, and South Asian populations. The p.Pro440= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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