rs4973588
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019850.3(NGEF):c.332T>G(p.Met111Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,605,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M111T) has been classified as Likely benign.
Frequency
Consequence
NM_019850.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NGEF | NM_019850.3 | c.332T>G | p.Met111Arg | missense_variant | 3/15 | ENST00000264051.8 | |
NGEF | XM_011510923.4 | c.332T>G | p.Met111Arg | missense_variant | 3/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NGEF | ENST00000264051.8 | c.332T>G | p.Met111Arg | missense_variant | 3/15 | 1 | NM_019850.3 | ||
NGEF | ENST00000414326.1 | c.239T>G | p.Met80Arg | missense_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152040Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1453400Hom.: 0 Cov.: 39 AF XY: 0.0000166 AC XY: 12AN XY: 723174
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152040Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74264
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at