2-232879643-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_019850.3(NGEF):c.1979G>A(p.Arg660Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 1,613,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019850.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NGEF | ENST00000264051.8 | c.1979G>A | p.Arg660Lys | missense_variant | Exon 15 of 15 | 1 | NM_019850.3 | ENSP00000264051.3 | ||
NGEF | ENST00000373552.8 | c.1703G>A | p.Arg568Lys | missense_variant | Exon 13 of 13 | 2 | ENSP00000362653.4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251168Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135810
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461036Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 726792
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1979G>A (p.R660K) alteration is located in exon 15 (coding exon 14) of the NGEF gene. This alteration results from a G to A substitution at nucleotide position 1979, causing the arginine (R) at amino acid position 660 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at