chrX-55001614-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_001271748.2(APEX2):c.-107C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.00000275 in 1,090,158 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001271748.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APEX2 | NM_014481.4 | c.226C>T | p.Arg76Cys | missense_variant | Exon 2 of 6 | ENST00000374987.4 | NP_055296.2 | |
APEX2 | NM_001271748.2 | c.-107C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 5 | NP_001258677.1 | |||
APEX2 | NM_001271748.2 | c.-107C>T | 5_prime_UTR_variant | Exon 2 of 5 | NP_001258677.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 0.00000275 AC: 3AN: 1090158Hom.: 0 Cov.: 29 AF XY: 0.00000561 AC XY: 2AN XY: 356196
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.226C>T (p.R76C) alteration is located in exon 2 (coding exon 2) of the APEX2 gene. This alteration results from a C to T substitution at nucleotide position 226, causing the arginine (R) at amino acid position 76 to be replaced by a cysteine (C). 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