chr2-232920507-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019850.3(NGEF):āc.605A>Cā(p.Glu202Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000264 in 1,593,732 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_019850.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NGEF | NM_019850.3 | c.605A>C | p.Glu202Ala | missense_variant | 5/15 | ENST00000264051.8 | |
NGEF | NM_001114090.2 | c.329A>C | p.Glu110Ala | missense_variant | 3/13 | ||
NGEF | XM_011510923.4 | c.605A>C | p.Glu202Ala | missense_variant | 5/15 | ||
NGEF | XM_047443880.1 | c.131A>C | p.Glu44Ala | missense_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NGEF | ENST00000264051.8 | c.605A>C | p.Glu202Ala | missense_variant | 5/15 | 1 | NM_019850.3 | ||
NGEF | ENST00000409079.1 | c.329A>C | p.Glu110Ala | missense_variant | 3/4 | 1 | |||
NGEF | ENST00000373552.8 | c.329A>C | p.Glu110Ala | missense_variant | 3/13 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000424 AC: 1AN: 235826Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127656
GnomAD4 exome AF: 0.0000264 AC: 38AN: 1441462Hom.: 1 Cov.: 33 AF XY: 0.0000294 AC XY: 21AN XY: 714314
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.605A>C (p.E202A) alteration is located in exon 5 (coding exon 4) of the NGEF gene. This alteration results from a A to C substitution at nucleotide position 605, causing the glutamic acid (E) at amino acid position 202 to be replaced by an alanine (A). 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