NM_001378609.3:c.3484G>A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001378609.3(OTOGL):c.3484G>A(p.Glu1162Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000558 in 1,612,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001378609.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTOGL | NM_001378609.3 | c.3484G>A | p.Glu1162Lys | missense_variant | Exon 31 of 59 | ENST00000547103.7 | NP_001365538.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.3484G>A | p.Glu1162Lys | missense_variant | Exon 31 of 59 | 5 | NM_001378609.3 | ENSP00000447211.2 | ||
OTOGL | ENST00000646859.1 | c.3349G>A | p.Glu1117Lys | missense_variant | Exon 35 of 63 | ENSP00000496036.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000406 AC: 10AN: 246498Hom.: 0 AF XY: 0.0000448 AC XY: 6AN XY: 133928
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1460166Hom.: 0 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 726440
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Glu1153Lys variant in OTOGL has not been previously reported in individual s with hearing loss, but has been identified in 4/55168 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs 374891321). Although this variant has been seen in the general population, its f requency is not high enough to rule out a pathogenic role. Computational predict ion tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogeni city. In summary, the clinical significance of the p.Glu1153Lys variant is uncer tain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at