11-17547541-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BS1BS2_Supporting
The NM_001277269.2(OTOG):c.169G>T(p.Ala57Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,277,382 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001277269.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000316 AC: 48AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000285 AC: 1AN: 3514Hom.: 0 AF XY: 0.000503 AC XY: 1AN XY: 1988
GnomAD4 exome AF: 0.000157 AC: 177AN: 1125150Hom.: 2 Cov.: 31 AF XY: 0.000160 AC XY: 86AN XY: 536268
GnomAD4 genome AF: 0.000315 AC: 48AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74420
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 30, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2025 | In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Sep 14, 2017 | p.Ala57Ser in exon 1 of OTOG: This variant is not expected to have clinical sign ificance because it has been identified in 0.8% (14/1838) of East Asian chromoso mes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org ; dbSNP rs550807341). - |
OTOG-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 27, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at