ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.989-3T>C

dbSNP: rs1156325177
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000629730 SCV000750686 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2023-10-22 criteria provided, single submitter clinical testing This sequence change falls in intron 9 of the PMS2 gene. It does not directly change the encoded amino acid sequence of the PMS2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PMS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 525619). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Mendelics RCV000708987 SCV000838183 uncertain significance Lynch syndrome 2018-07-02 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000777103 SCV000912789 uncertain significance Hereditary cancer-predisposing syndrome 2018-12-21 criteria provided, single submitter clinical testing
Ambry Genetics RCV000777103 SCV004092414 uncertain significance Hereditary cancer-predisposing syndrome 2023-07-03 criteria provided, single submitter clinical testing The c.989-3T>C intronic variant results from a T to C substitution 3 nucleotides upstream from coding exon 10 in the PMS2 gene. This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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