ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.877G>A (p.Ala293Thr) (rs782239416)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000431253 SCV000528475 likely benign not specified 2016-06-16 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.
Genetic Services Laboratory,University of Chicago RCV000431253 SCV000595737 uncertain significance not specified 2016-08-01 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000431253 SCV000919624 likely benign not specified 2018-11-28 criteria provided, single submitter clinical testing Variant summary: MECP2 c.841G>A (p.Ala281Thr) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 9.6e-05 in 176575 control chromosomes, including 7 hemizygotes (gnomAD). The observed variant frequency is approximately 11.5 folds higher than the estimated maximal expected allele frequency for a pathogenic variant in MECP2 causing Rett Syndrome phenotype (8.3e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.841G>A in individuals affected with Rett Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely benign and uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.
Invitae RCV000873957 SCV001016060 benign not provided 2018-09-11 criteria provided, single submitter clinical testing

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