ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.1269C>T (p.Ser423=)

gnomAD frequency: 0.01726  dbSNP: rs3027928
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000081196 SCV000113104 benign not specified 2017-10-05 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000081196 SCV000247943 benign not specified 2013-02-08 criteria provided, single submitter clinical testing
Preventiongenetics, part of Exact Sciences RCV000081196 SCV000310759 benign not specified criteria provided, single submitter clinical testing
Invitae RCV000464380 SCV000556735 benign Severe neonatal-onset encephalopathy with microcephaly 2024-02-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000587510 SCV000604149 benign not provided 2021-08-09 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000587510 SCV000698535 benign not provided 2016-03-24 criteria provided, single submitter clinical testing Variant Summary: The variant of interest causes a synonymous change involving a non-conserved nucleotide with 5/5 in silico programs via Alamut predicting no significant effect on splicing. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 2425/86448 (1/35 including 248 homozygotes and 583 hemizygotes), which significantly exceeds the predicted maximum expected allele frequency for a pathogenic MECP2 variant of 1/120481. In addition, multiple reputable database/clinical laboratories cite the variant with a classification of "benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
Ambry Genetics RCV000715138 SCV000845965 benign History of neurodevelopmental disorder 2014-11-24 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: 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.
GeneDx RCV000587510 SCV001907434 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587510 SCV002774016 benign not provided 2021-10-04 criteria provided, single submitter clinical testing
Centre for Population Genomics, CPG RCV003380413 SCV004098745 benign Rett syndrome 2023-08-14 criteria provided, single submitter curation This variant has been collected from RettBASE and curated to current modified ACMG/AMP criteria.Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 2.0, this variant is classified as benign. At least the following criteria are met: The allele frequency of this variant in at least one population in gnomAD is higher than the 0.03% threshold defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders VCEP 2.0 (BA1). Synonymous or intronic variant outside donor and acceptor splice regions where splicing prediction algorithms do not support significant splicing alteration (spliceAI score <=0.1) (BP4, BP7).
RettBASE RCV000081196 SCV000187956 benign not specified 2013-12-05 no assertion criteria provided curation

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