chr8-6642993-G-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_024596.5(MCPH1):c.2453-1G>A variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.0000143 in 1,613,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_024596.5 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MCPH1 | NM_024596.5 | c.2453-1G>A | splice_acceptor_variant, intron_variant | ENST00000344683.10 | NP_078872.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCPH1 | ENST00000344683.10 | c.2453-1G>A | splice_acceptor_variant, intron_variant | 1 | NM_024596.5 | ENSP00000342924.5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249366Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135296
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461662Hom.: 0 Cov.: 29 AF XY: 0.0000179 AC XY: 13AN XY: 727146
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at