3-9750981-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_002542.6(OGG1):c.174A>T(p.Val58Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000226 in 1,614,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_002542.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251270Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135806
GnomAD4 exome AF: 0.000233 AC: 341AN: 1461818Hom.: 0 Cov.: 31 AF XY: 0.000220 AC XY: 160AN XY: 727202
GnomAD4 genome AF: 0.000151 AC: 23AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74352
ClinVar
Submissions by phenotype
OGG1-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