chr14-20456854-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001641.4(APEX1):c.433G>A(p.Gly145Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,613,686 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APEX1 | NM_001641.4 | c.433G>A | p.Gly145Ser | missense_variant | Exon 4 of 5 | ENST00000216714.8 | NP_001632.2 | |
APEX1 | NM_001244249.2 | c.433G>A | p.Gly145Ser | missense_variant | Exon 4 of 5 | NP_001231178.1 | ||
APEX1 | NM_080648.3 | c.433G>A | p.Gly145Ser | missense_variant | Exon 4 of 5 | NP_542379.1 | ||
APEX1 | NM_080649.3 | c.433G>A | p.Gly145Ser | missense_variant | Exon 4 of 5 | NP_542380.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000225 AC: 56AN: 249216Hom.: 2 AF XY: 0.000304 AC XY: 41AN XY: 134796
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461510Hom.: 2 Cov.: 32 AF XY: 0.000153 AC XY: 111AN XY: 727024
GnomAD4 genome AF: 0.000138 AC: 21AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.433G>A (p.G145S) 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 433, causing the glycine (G) at amino acid position 145 to be replaced by a serine (S). 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