rs2734647
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001110792.2(MECP2):c.*3638A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.83 ( 28176 hom., 26347 hem., cov: 23)
Exomes 𝑓: 0.88 ( 77 hom. 131 hem. )
Failed GnomAD Quality Control
Consequence
MECP2
NM_001110792.2 3_prime_UTR
NM_001110792.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.815
Genes affected
MECP2 (HGNC:6990): (methyl-CpG binding protein 2) DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. In contrast to other MBD family members, MECP2 is X-linked and subject to X inactivation. MECP2 is dispensible in stem cells, but is essential for embryonic development. MECP2 gene mutations are the cause of most cases of Rett syndrome, a progressive neurologic developmental disorder and one of the most common causes of cognitive disability in females. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant X-154026729-T-C is Benign according to our data. Variant chrX-154026729-T-C is described in Lovd as [Likely_benign].
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MECP2 | NM_001110792.2 | c.*3638A>G | 3_prime_UTR_variant | 3/3 | ENST00000453960.7 | ||
MECP2 | NM_004992.4 | c.*3638A>G | 3_prime_UTR_variant | 4/4 | ENST00000303391.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MECP2 | ENST00000303391.11 | c.*3638A>G | 3_prime_UTR_variant | 4/4 | 1 | NM_004992.4 | P1 | ||
MECP2 | ENST00000453960.7 | c.*3638A>G | 3_prime_UTR_variant | 3/3 | 1 | NM_001110792.2 |
Frequencies
GnomAD3 genomes AF: 0.827 AC: 91325AN: 110435Hom.: 28174 Cov.: 23 AF XY: 0.806 AC XY: 26286AN XY: 32609
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GnomAD4 exome AF: 0.875 AC: 309AN: 353Hom.: 77 Cov.: 0 AF XY: 0.868 AC XY: 131AN XY: 151
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.827 AC: 91383AN: 110489Hom.: 28176 Cov.: 23 AF XY: 0.806 AC XY: 26347AN XY: 32673
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at