chr11-17547465-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001292063.2(OTOG):c.93C>T(p.Leu31Leu) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000937 in 1,366,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001292063.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.93C>T | p.Leu31Leu | splice_region_variant, synonymous_variant | Exon 1 of 56 | 5 | NM_001292063.2 | ENSP00000382329.2 | ||
OTOG | ENST00000399391.7 | c.93C>T | p.Leu31Leu | synonymous_variant | Exon 1 of 55 | 5 | ENSP00000382323.2 |
Frequencies
GnomAD3 genomes AF: 0.000178 AC: 27AN: 151932Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000832 AC: 101AN: 1214454Hom.: 0 Cov.: 31 AF XY: 0.0000864 AC XY: 51AN XY: 589954
GnomAD4 genome AF: 0.000178 AC: 27AN: 151932Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74204
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
- -
Has not been previously published as pathogenic or benign to our knowledge; In-silico analysis, which includes splice predictors and evolutionary conservation, 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