rs397515427
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_001271938.2(MEGF8):c.4697G>A(p.Arg1566His) variant causes a missense change. The variant allele was found at a frequency of 0.00000826 in 1,574,266 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 Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1566C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001271938.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEGF8 | NM_001271938.2 | c.4697G>A | p.Arg1566His | missense_variant | 27/42 | ENST00000251268.11 | |
MEGF8 | NM_001410.3 | c.4496G>A | p.Arg1499His | missense_variant | 26/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEGF8 | ENST00000251268.11 | c.4697G>A | p.Arg1566His | missense_variant | 27/42 | 5 | NM_001271938.2 | A2 | |
MEGF8 | ENST00000334370.8 | c.4496G>A | p.Arg1499His | missense_variant | 26/41 | 1 | P2 | ||
MEGF8 | ENST00000378073.5 | c.-2389G>A | 5_prime_UTR_variant | 27/41 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000844 AC: 12AN: 1422074Hom.: 0 Cov.: 32 AF XY: 0.00000995 AC XY: 7AN XY: 703740
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
MEGF8-related Carpenter syndrome Pathogenic:2
Likely pathogenic, no assertion criteria provided | clinical testing | Wilkie Group, Clinical Genetics Lab, WIMM, University of Oxford | - | - - |
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