12-80355790-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001378609.3(OTOGL):c.5648G>A(p.Gly1883Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000188 in 1,613,788 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1883S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378609.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOGL | NM_001378609.3 | c.5648G>A | p.Gly1883Asp | missense_variant | 47/59 | ENST00000547103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.5648G>A | p.Gly1883Asp | missense_variant | 47/59 | 5 | NM_001378609.3 | P1 | |
OTOGL | ENST00000646859.1 | c.5513G>A | p.Gly1838Asp | missense_variant | 51/63 | ||||
OTOGL | ENST00000298820.7 | c.950G>A | p.Gly317Asp | missense_variant | 8/18 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000268 AC: 66AN: 246476Hom.: 1 AF XY: 0.000336 AC XY: 45AN XY: 133920
GnomAD4 exome AF: 0.000190 AC: 278AN: 1461564Hom.: 1 Cov.: 31 AF XY: 0.000228 AC XY: 166AN XY: 727050
GnomAD4 genome AF: 0.000164 AC: 25AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74426
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 18, 2015 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 02, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at