ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.706-3C>T

gnomAD frequency: 0.00030  dbSNP: rs1229860023
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000584358 SCV000691099 likely benign Hereditary cancer-predisposing syndrome 2017-06-02 criteria provided, single submitter clinical testing
Invitae RCV000630290 SCV000751246 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2019-06-28 criteria provided, single submitter clinical testing 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. Nucleotide substitutions within 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, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with PMS2-related disease. ClinVar contains an entry for this variant (Variation ID: 492288). This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 6 of the PMS2 gene. It does not directly change the encoded amino acid sequence of the PMS2 protein, but it affects a nucleotide within the consensus splice site of the intron.
Mendelics RCV000987845 SCV001137319 likely benign Lynch syndrome 4 2019-05-28 criteria provided, single submitter clinical testing
Ambry Genetics RCV000584358 SCV001188284 likely benign Hereditary cancer-predisposing syndrome 2020-03-04 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
All of Us Research Program, National Institutes of Health RCV004002368 SCV004821468 likely benign Lynch syndrome 2023-10-30 criteria provided, single submitter clinical testing

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