chr14-20457358-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001641.4(APEX1):āc.807T>Cā(p.Tyr269Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000777 in 1,614,240 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001641.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APEX1 | NM_001641.4 | c.807T>C | p.Tyr269Tyr | synonymous_variant | Exon 5 of 5 | ENST00000216714.8 | NP_001632.2 | |
APEX1 | NM_001244249.2 | c.807T>C | p.Tyr269Tyr | synonymous_variant | Exon 5 of 5 | NP_001231178.1 | ||
APEX1 | NM_080648.3 | c.807T>C | p.Tyr269Tyr | synonymous_variant | Exon 5 of 5 | NP_542379.1 | ||
APEX1 | NM_080649.3 | c.807T>C | p.Tyr269Tyr | synonymous_variant | Exon 5 of 5 | NP_542380.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00347 AC: 528AN: 152230Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000863 AC: 217AN: 251492Hom.: 1 AF XY: 0.000728 AC XY: 99AN XY: 135920
GnomAD4 exome AF: 0.000495 AC: 723AN: 1461892Hom.: 3 Cov.: 33 AF XY: 0.000446 AC XY: 324AN XY: 727246
GnomAD4 genome AF: 0.00349 AC: 531AN: 152348Hom.: 2 Cov.: 32 AF XY: 0.00332 AC XY: 247AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:1
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APEX1-related disorder Benign:1
This variant is classified as likely 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