ClinVar Miner

Submissions for variant NM_000245.4(MET):c.3858C>T (p.Asp1286=)

gnomAD frequency: 0.33828  dbSNP: rs41736
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 15
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000079492 SCV000111374 benign not specified 2014-07-30 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162950 SCV000213437 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 RCV000079492 SCV000306715 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000351242 SCV000466459 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 RCV000079492 SCV000513600 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 RCV001507219 SCV000623442 benign Renal cell carcinoma 2024-02-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589523 SCV000697660 benign not provided 2016-08-18 criteria provided, single submitter clinical testing Variant summary: The MET c.3912C>T (p.Asp1304Asp) 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. 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 51052/120736 control chromosomes (11511 homozygotes) at a frequency of 0.4228399, which is approximately 281893 times the estimated maximal expected allele frequency of a pathogenic MET variant (0.0000015), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Genome-Nilou Lab RCV001775570 SCV002014199 benign Autosomal recessive nonsyndromic hearing loss 97 2021-09-05 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000351242 SCV004015831 benign Papillary renal cell carcinoma type 1 2023-07-07 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000589523 SCV005273294 benign not provided criteria provided, single submitter not provided
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000351242 SCV005442080 benign Papillary renal cell carcinoma type 1 2024-12-19 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000079492 SCV001743587 benign not specified no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000079492 SCV001918888 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000079492 SCV001929584 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000079492 SCV001956688 benign not specified no assertion criteria provided clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.