rs397514621
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001271938.2(MEGF8):c.1342C>T(p.Arg448Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001271938.2 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEGF8 | NM_001271938.2 | c.1342C>T | p.Arg448Ter | stop_gained | 7/42 | ENST00000251268.11 | |
MEGF8 | NM_001410.3 | c.1342C>T | p.Arg448Ter | stop_gained | 7/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEGF8 | ENST00000251268.11 | c.1342C>T | p.Arg448Ter | stop_gained | 7/42 | 5 | NM_001271938.2 | A2 | |
MEGF8 | ENST00000334370.8 | c.1342C>T | p.Arg448Ter | stop_gained | 7/41 | 1 | P2 | ||
MEGF8 | ENST00000378073.5 | c.-5744C>T | 5_prime_UTR_variant | 7/41 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250568Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135484
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461360Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726996
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74264
ClinVar
Submissions by phenotype
MEGF8-related Carpenter syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 02, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at