ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.2265C>T (p.Ile755=)

gnomAD frequency: 0.00001  dbSNP: rs145646046
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000205449 SCV000260696 likely benign Hereditary nonpolyposis colorectal neoplasms 2024-01-28 criteria provided, single submitter clinical testing
Ambry Genetics RCV000222777 SCV000273801 likely benign Hereditary cancer-predisposing syndrome 2015-02-06 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.
CeGaT Center for Human Genetics Tuebingen RCV001200526 SCV001371511 likely benign not provided 2022-06-01 criteria provided, single submitter clinical testing PMS2: BP4, BP7
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001526981 SCV001737772 likely benign not specified 2021-06-05 criteria provided, single submitter clinical testing
GeneDx RCV001200526 SCV001861959 likely benign not provided 2020-09-09 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV001200526 SCV004218981 benign not provided 2023-07-03 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000222777 SCV004359024 benign Hereditary cancer-predisposing syndrome 2022-03-10 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001200526 SCV001549074 likely benign not provided no assertion criteria provided clinical testing The PMS2 p.Ile755= variant was not identified in the literature nor was it identified in the COGR, Cosmic, MutDB, Insight Colon Cancer Gene Variant Database, Zhejiang University Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors Database. The variant was identified in dbSNP (ID: rs145646046) as “With Likely benign allele”, ClinVar (as likely benign by Invitae and Ambry Genetics), and Clinvitae databases. The variant was identified in control databases in 24 of 244310 chromosomes (2 homozygous) at a frequency of 0.0001 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: South Asian in 21 of 30634 chromosomes (freq: 0.0007) and European (Non-Finnish) in 3 of 110376 chromosomes (freq: 0.00003); it was not observed in the African, Other, Latino, Ashkenazi Jewish, East Asian, or Finnish populations. The p.Ile755= 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 addition, 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts a greater than 10% difference in splicing 5bp upstream of this variant, however, this information is not very predictive of pathogenicity. In summary, the clinical significance of this variant cannot be determined with certainty at this time, although the available information suggests a benign role for this variant. This variant is classified as likely benign.

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