14-20457017-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001641.4(APEX1):c.466C>T(p.Arg156Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000991 in 1,613,920 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.466C>T | p.Arg156Trp | missense_variant | Exon 5 of 5 | ENST00000216714.8 | NP_001632.2 | |
APEX1 | NM_001244249.2 | c.466C>T | p.Arg156Trp | missense_variant | Exon 5 of 5 | NP_001231178.1 | ||
APEX1 | NM_080648.3 | c.466C>T | p.Arg156Trp | missense_variant | Exon 5 of 5 | NP_542379.1 | ||
APEX1 | NM_080649.3 | c.466C>T | p.Arg156Trp | missense_variant | Exon 5 of 5 | NP_542380.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250834Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135626
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461772Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727178
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.466C>T (p.R156W) alteration is located in exon 5 (coding exon 4) of the APEX1 gene. This alteration results from a C to T substitution at nucleotide position 466, causing the arginine (R) at amino acid position 156 to be replaced by a tryptophan (W). 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