19-45529214-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001017989.3(OPA3):āc.385T>Cā(p.Leu129Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000992 in 1,612,400 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_001017989.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000204 AC: 5AN: 245080Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133542
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460116Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726478
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152284Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74462
ClinVar
Submissions by phenotype
OPA3-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