14-20457272-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001641.4(APEX1):c.721G>A(p.Gly241Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00101 in 1,614,210 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001641.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APEX1 | NM_001641.4 | c.721G>A | p.Gly241Arg | missense_variant | Exon 5 of 5 | ENST00000216714.8 | NP_001632.2 | |
APEX1 | NM_001244249.2 | c.721G>A | p.Gly241Arg | missense_variant | Exon 5 of 5 | NP_001231178.1 | ||
APEX1 | NM_080648.3 | c.721G>A | p.Gly241Arg | missense_variant | Exon 5 of 5 | NP_542379.1 | ||
APEX1 | NM_080649.3 | c.721G>A | p.Gly241Arg | missense_variant | Exon 5 of 5 | NP_542380.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00520 AC: 792AN: 152202Hom.: 11 Cov.: 33
GnomAD3 exomes AF: 0.00138 AC: 348AN: 251496Hom.: 3 AF XY: 0.00100 AC XY: 136AN XY: 135922
GnomAD4 exome AF: 0.000575 AC: 840AN: 1461890Hom.: 9 Cov.: 33 AF XY: 0.000498 AC XY: 362AN XY: 727246
GnomAD4 genome AF: 0.00519 AC: 791AN: 152320Hom.: 11 Cov.: 33 AF XY: 0.00506 AC XY: 377AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
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APEX1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at