ClinVar Miner

Submissions for variant NM_000245.4(MET):c.1975A>T (p.Ile659Leu)

gnomAD frequency: 0.00014  dbSNP: rs753958204
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000466935 SCV000553332 likely benign Renal cell carcinoma 2024-01-24 criteria provided, single submitter clinical testing
Ambry Genetics RCV001013811 SCV001174442 likely benign Hereditary cancer-predisposing syndrome 2022-04-08 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.
GeneDx RCV001547636 SCV001767390 uncertain significance not provided 2023-08-29 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Identified in an individual with renal cell carcinoma (Yehia et al., 2018); This variant is associated with the following publications: (PMID: 29684080)
Quest Diagnostics Nichols Institute San Juan Capistrano RCV001547636 SCV005622895 uncertain significance not provided 2024-11-15 criteria provided, single submitter clinical testing The MET c.1975A>T (p.Ile659Leu) variant has been reported in the published literature in an individual with Cowden syndrome/Cowden-like syndrome or Bannayan-Riley-Ruvalcaba syndrome (PMID: 29684080 (2018)). The frequency of this variant in the general population, 0.00033 (8/24202 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is benign or damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

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