ClinVar Miner

Submissions for variant NM_000249.3(MLH1):c.1164C>T (p.Ser388=) (rs1060504014)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000572315 SCV000662043 likely benign Hereditary cancer-predisposing syndrome 2015-10-30 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Synonymous alterations with insufficient evidence to classify as benign,In silico models in agreement (benign)
Color RCV000572315 SCV000684722 likely benign Hereditary cancer-predisposing syndrome 2016-05-29 criteria provided, single submitter clinical testing
GeneDx RCV000612351 SCV000716574 likely benign not specified 2017-03-01 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.
Integrated Genetics/Laboratory Corporation of America RCV000612351 SCV000919635 uncertain significance not specified 2017-11-06 criteria provided, single submitter clinical testing Variant summary: The MLH1 c.1164C>T (p.Ser388Ser) variant involves the alteration of a non-conserved nucleotide causing a synonymous change and 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may alter ESE binding. However, these predictions have yet to be confirmed by functional studies. This variant was found in 2/30788 control chromosomes (gnomAD) at a frequency of 0.000065, which does not exceed the estimated maximal expected allele frequency of a pathogenic MLH1 variant (0.0007105). In addition, a clinical diagnostic laboratory classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as a "Variant of Uncertain Significance - Possibly Benign," until additional information becomes available (ie, clinical and functional studies).
Invitae RCV000460062 SCV000556010 likely benign Lynch syndrome 2016-12-22 criteria provided, single submitter clinical testing

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