rs886037828
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_025136.4(OPA3):c.235C>T(p.Leu79=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,460,962 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 (★). Synonymous variant affecting the same amino acid position (i.e. L79L) has been classified as Likely benign.
Frequency
Consequence
NM_025136.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPA3 | NM_025136.4 | c.235C>T | p.Leu79= | synonymous_variant | 2/2 | ENST00000263275.5 | |
OPA3 | XM_006723403.5 | c.76C>T | p.Leu26= | synonymous_variant | 3/3 | ||
OPA3 | NM_001017989.3 | c.143-24363C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPA3 | ENST00000263275.5 | c.235C>T | p.Leu79= | synonymous_variant | 2/2 | 1 | NM_025136.4 | P1 | |
OPA3 | ENST00000323060.4 | c.143-24363C>T | intron_variant | 1 | |||||
OPA3 | ENST00000544371.1 | c.76C>T | p.Leu26= | synonymous_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1460962Hom.: 0 Cov.: 62 AF XY: 0.00 AC XY: 0AN XY: 726804
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
3-Methylglutaconic aciduria type 3;C1833809:Optic atrophy 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at