ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.164-4C>A

dbSNP: rs876658444
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000220376 SCV000273654 likely benign Hereditary cancer-predisposing syndrome 2017-07-31 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.
Invitae RCV000630356 SCV000751312 likely benign Hereditary nonpolyposis colorectal neoplasms 2024-01-22 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001358033 SCV001553670 uncertain significance Carcinoma of colon no assertion criteria provided clinical testing The PMS2 c.164-4C>A variant was not identified in the literature. The variant was identified in dbSNP (rs876658444) as “with likely benign allele” and ClinVar (classified as likely benign by Ambry Genetics and Invitae). The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). The c.164-4C>A variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions nor does it affect positions -3 and -5 to -12, which are also part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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