rs61754422
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001110792.2(MECP2):c.72G>T(p.Lys24Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,201,519 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001110792.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MECP2 | NM_001110792.2 | c.72G>T | p.Lys24Asn | missense_variant | 2/3 | ENST00000453960.7 | |
MECP2 | NM_004992.4 | c.36G>T | p.Lys12Asn | missense_variant | 3/4 | ENST00000303391.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MECP2 | ENST00000453960.7 | c.72G>T | p.Lys24Asn | missense_variant | 2/3 | 1 | NM_001110792.2 | ||
MECP2 | ENST00000303391.11 | c.36G>T | p.Lys12Asn | missense_variant | 3/4 | 1 | NM_004992.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000887 AC: 1AN: 112715Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34849
GnomAD3 exomes AF: 0.00000567 AC: 1AN: 176350Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 65056
GnomAD4 exome AF: 0.00000184 AC: 2AN: 1088804Hom.: 0 Cov.: 30 AF XY: 0.00000280 AC XY: 1AN XY: 357770
GnomAD4 genome ? AF: 0.00000887 AC: 1AN: 112715Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34849
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at