rs761265704
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001641.4(APEX1):c.391G>A(p.Val131Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000799 in 1,614,096 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 Uncertain significance (★).
Frequency
Consequence
NM_001641.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APEX1 | NM_001641.4 | c.391G>A | p.Val131Met | missense_variant | Exon 4 of 5 | ENST00000216714.8 | NP_001632.2 | |
APEX1 | NM_001244249.2 | c.391G>A | p.Val131Met | missense_variant | Exon 4 of 5 | NP_001231178.1 | ||
APEX1 | NM_080648.3 | c.391G>A | p.Val131Met | missense_variant | Exon 4 of 5 | NP_542379.1 | ||
APEX1 | NM_080649.3 | c.391G>A | p.Val131Met | missense_variant | Exon 4 of 5 | NP_542380.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 250936Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135688
GnomAD4 exome AF: 0.0000780 AC: 114AN: 1461852Hom.: 0 Cov.: 32 AF XY: 0.0000770 AC XY: 56AN XY: 727228
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.391G>A (p.V131M) alteration is located in exon 4 (coding exon 3) of the APEX1 gene. This alteration results from a G to A substitution at nucleotide position 391, causing the valine (V) at amino acid position 131 to be replaced by a methionine (M). 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