ClinVar Miner

Submissions for variant NM_000245.4(MET):c.1131C>T (p.Ile377=)

gnomAD frequency: 0.05590  dbSNP: rs28444388
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Total submissions: 16
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000079483 SCV000111363 benign not specified 2012-09-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162959 SCV000213447 benign Hereditary cancer-predisposing syndrome 2014-11-21 criteria provided, single submitter clinical testing This alteration is classified as 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.
PreventionGenetics, part of Exact Sciences RCV000079483 SCV000306707 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000280048 SCV000466438 benign Papillary renal cell carcinoma type 1 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000079483 SCV000518948 benign not specified 2016-03-01 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV001507224 SCV000563136 benign Renal cell carcinoma 2024-02-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589420 SCV000697657 benign not provided 2016-08-18 criteria provided, single submitter clinical testing Variant summary: The MET c.1131C>T (p.Ile377Ile) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a polymorphism outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE site of SRp40. This variant was found in 2192/116598 control chromosomes (215 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.2046621 (1993/9738). This frequency is about 136441 times the estimated maximal expected allele frequency of a pathogenic MET variant (0.0000015), suggesting this is a common benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Athena Diagnostics RCV000589420 SCV000842762 benign not provided 2018-05-23 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000589420 SCV001157088 benign not provided 2023-11-29 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000162959 SCV002532095 benign Hereditary cancer-predisposing syndrome 2021-05-19 criteria provided, single submitter curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000079483 SCV002550782 benign not specified 2023-08-15 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589420 SCV002774019 benign not provided 2022-04-28 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000280048 SCV004015839 benign Papillary renal cell carcinoma type 1 2023-07-07 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000589420 SCV005273283 benign not provided criteria provided, single submitter not provided
Clinical Genetics, Academic Medical Center RCV000079483 SCV001918209 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000079483 SCV001957687 benign not specified no assertion criteria provided clinical testing

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