chr19-45529153-AG-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_Strong
The NM_001017989.3(OPA3):βc.445delCβ(p.Leu149TrpfsTer67) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,609,686 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β β ).
Frequency
Consequence
NM_001017989.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000844 AC: 2AN: 236950Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 130204
GnomAD4 exome AF: 0.00000961 AC: 14AN: 1457538Hom.: 0 Cov.: 31 AF XY: 0.00000827 AC XY: 6AN XY: 725228
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74340
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.445delC (p.L149Wfs*67) alteration, located in exon 2 (coding exon 2) of the OPA3 gene, consists of a deletion of one nucleotide at position 445, causing a translational frameshift with a predicted alternate stop codon after 67 amino acids. Frameshift alterations are typically deleterious in nature (Richards, 2015). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
3-Methylglutaconic aciduria type 3;C1833809:Optic atrophy 3 Uncertain:1
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3-Methylglutaconic aciduria type 3 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at