ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.354-34C>G

gnomAD frequency: 0.00049  dbSNP: rs200029834
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV002268568 SCV002550753 likely benign not specified 2023-08-15 criteria provided, single submitter clinical testing
Invitae RCV002539745 SCV003471496 likely benign Hereditary nonpolyposis colorectal neoplasms 2022-11-14 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003407777 SCV004114825 uncertain significance PMS2-related disorder 2022-11-30 criteria provided, single submitter clinical testing The PMS2 c.11C>G variant is predicted to result in premature protein termination (p.Ser4*). However, this variant is located in the first coding exon of a non-canonical transcript (NM_001322015.1). Using the most commonly reported PMS2 canonical transcript (NM_000535.6) this variant is located in intron 4, and called c.354-34C>G. This variant has been reported in individuals with renal cell carcinoma but no additional studies supported its pathogenicity (Smith et al. 2021. PubMed ID: 32830346). This variant is reported in 0.043% of alleles in individuals of European (Non-Finnish) descent in gnomAD, which is higher than expected for a pathogenic variant in this gene (; 70 total heterozygous individuals of unknown phenotype). It is reported as likely benign by multiple labs in ClinVar. Although we expect this alteration is more likely to be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV001723272 SCV001956669 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001723272 SCV001965414 likely benign not provided no assertion criteria provided clinical testing

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