2-232884085-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019850.3(NGEF):c.1497G>A(p.Met499Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,876 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NGEF | ENST00000264051.8 | c.1497G>A | p.Met499Ile | missense_variant | Exon 11 of 15 | 1 | NM_019850.3 | ENSP00000264051.3 | ||
NGEF | ENST00000373552.8 | c.1221G>A | p.Met407Ile | missense_variant | Exon 9 of 13 | 2 | ENSP00000362653.4 | |||
NGEF | ENST00000424488.5 | c.153G>A | p.Met51Ile | missense_variant | Exon 4 of 6 | 3 | ENSP00000387591.2 | |||
NGEF | ENST00000489127.1 | n.317G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459876Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726132
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1497G>A (p.M499I) alteration is located in exon 11 (coding exon 10) of the NGEF gene. This alteration results from a G to A substitution at nucleotide position 1497, causing the methionine (M) at amino acid position 499 to be replaced by an isoleucine (I). 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