ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.705+12C>T

gnomAD frequency: 0.00004  dbSNP: rs368486366
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000417561 SCV000514194 benign not specified 2015-08-18 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Color Diagnostics, LLC DBA Color Health RCV000580715 SCV000686228 likely benign Hereditary cancer-predisposing syndrome 2017-03-19 criteria provided, single submitter clinical testing
Invitae RCV002061467 SCV002430170 likely benign Hereditary nonpolyposis colorectal neoplasms 2024-02-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001358403 SCV001554123 likely benign Lynch syndrome no assertion criteria provided clinical testing The PMS2 c.705+12C>T variant was not identified in the literature. The variant was identified in dbSNP (ID: rs368486366) as "With Likely benign allele" and ClinVar (classified as benign by GeneDx; as likely benign by Color). The variant was identified in control databases in 6 of 246260 chromosomes at a frequency of 0.00002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 4 of 15304 chromosomes (freq: 0.0003, increasing the likelihood that this could be a low frequency benign variant) and Latino in 2 of 33582 chromosomes (freq: 0.00006), while it was not observed in the Other, European, Ashkenazi Jewish, East Asian, Finnish, or South Asian populations. The variant occurs outside of the splicing consensus sequence and 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 although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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