ClinVar Miner

Submissions for variant NM_000245.4(MET):c.4017G>A (p.Ala1339=)

gnomAD frequency: 0.34017  dbSNP: rs2023748
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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000079493 SCV000111375 benign not specified 2014-07-30 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162951 SCV000213438 benign Hereditary cancer-predisposing syndrome 2014-11-19 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 RCV000079493 SCV000306716 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000389579 SCV000466460 benign Papillary renal cell carcinoma type 1 2018-01-13 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 RCV000079493 SCV000513601 benign not specified 2016-01-19 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 RCV001507220 SCV000623448 benign Renal cell carcinoma 2024-02-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586311 SCV000697661 benign not provided 2016-08-19 criteria provided, single submitter clinical testing Variant summary: The c.4071G>A (p.Ala1357=) in MET gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.4245 (51253/120730chrs tested) including numerous homozygous occurrences. The variant of interest has not, to our knowledge, been reported in affected individuals via publication but is cited as Benign by reputable databases/clinical laboratories. Taking together, based on the prevalence of this variant in general population the variant was classified as Benign.
Genome-Nilou Lab RCV001775571 SCV002014200 benign Autosomal recessive nonsyndromic hearing loss 97 2021-09-05 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000389579 SCV004015832 benign Papillary renal cell carcinoma type 1 2023-07-07 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000586311 SCV005273295 benign not provided criteria provided, single submitter not provided
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000079493 SCV001743666 benign not specified no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000079493 SCV001921318 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000079493 SCV001930928 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000079493 SCV001959697 benign not specified no assertion criteria provided clinical testing

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