rs3027939
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000453960.7(MECP2):c.63-12570T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0967 in 111,902 control chromosomes in the GnomAD database, including 683 homozygotes. There are 2,926 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.
Frequency
Consequence
ENST00000453960.7 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MECP2 | NM_001110792.2 | c.63-12570T>C | intron_variant | ENST00000453960.7 | NP_001104262.1 | |||
MECP2 | NM_004992.4 | c.27-12570T>C | intron_variant | ENST00000303391.11 | NP_004983.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MECP2 | ENST00000303391.11 | c.27-12570T>C | intron_variant | 1 | NM_004992.4 | ENSP00000301948 | P1 | |||
MECP2 | ENST00000453960.7 | c.63-12570T>C | intron_variant | 1 | NM_001110792.2 | ENSP00000395535 |
Frequencies
GnomAD3 genomes AF: 0.0965 AC: 10791AN: 111850Hom.: 680 Cov.: 23 AF XY: 0.0856 AC XY: 2913AN XY: 34040
GnomAD4 genome AF: 0.0967 AC: 10817AN: 111902Hom.: 683 Cov.: 23 AF XY: 0.0858 AC XY: 2926AN XY: 34102
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at