19-45529145-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_001017989.3(OPA3):c.454C>T(p.Leu152Leu) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000988 in 1,609,392 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001017989.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000182 AC: 43AN: 236892Hom.: 0 AF XY: 0.000215 AC XY: 28AN XY: 130248
GnomAD4 exome AF: 0.000104 AC: 152AN: 1457198Hom.: 0 Cov.: 31 AF XY: 0.000110 AC XY: 80AN XY: 724876
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74354
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
OPA3: BP4, BP7 -
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at