ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.1216G>A (p.Glu406Lys) (rs63094662)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000132947 SCV000515675 likely benign not specified 2016-08-23 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.
Molecular Diagnostics Lab,Nemours Alfred I. duPont Hospital for Children RCV000445563 SCV000537179 benign Rett syndrome 2015-07-09 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000132947 SCV000919614 benign not specified 2017-10-12 criteria provided, single submitter clinical testing Variant summary: The MECP2 c.1180G>A (p.Glu394Lys) variant involves the alteration of a non-conserved nucleotide and 3/4 in silico tools (Mutation Taster not captured here due to low p-value) predict a benign outcome for this variant. This variant was found in 13/184110 (5 hemizygotes) control chromosomes (gnomAD) at a frequency of 0.0000706, which is approximately 8 times the estimated maximal expected allele frequency of a pathogenic MECP2 variant (0.0000083), suggesting this variant is likely a benign polymorphism. A publication reported a RETT syndrome patient who carried another pathogenic MECP2 variant p.Arg168X and the patient's unaffected father also carried the variant of interest (Chapleau_2013), strongly supporting benign outcome. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign/benign. Taken together, this variant is classified as benign.
RettBASE RCV000132947 SCV000187928 benign not specified 2014-02-05 no assertion criteria provided curation

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