ClinVar Miner

Submissions for variant NM_001127500.3(MET):c.3912C>T (p.Asp1304=) (rs41736)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 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
PreventionGenetics,PreventionGenetics RCV000079492 SCV000306715 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000351242 SCV000466459 benign Renal cell carcinoma, papillary, 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.
Invitae RCV000351242 SCV000623442 benign Renal cell carcinoma, papillary, 1 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America 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.

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