rs201869161
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001378609.3(OTOGL):c.6055C>A(p.His2019Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000366 in 1,612,214 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001378609.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOGL | NM_001378609.3 | c.6055C>A | p.His2019Asn | missense_variant | 50/59 | ENST00000547103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.6055C>A | p.His2019Asn | missense_variant | 50/59 | 5 | NM_001378609.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000863 AC: 213AN: 246872Hom.: 5 AF XY: 0.00107 AC XY: 143AN XY: 133540
GnomAD4 exome AF: 0.000381 AC: 556AN: 1459990Hom.: 8 Cov.: 30 AF XY: 0.000530 AC XY: 385AN XY: 726140
GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74416
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 27, 2016 | p.His2010Asn in exon 49 of OTOGL: This variant is not expected to have clinical significance because it has been identified in 0.84% (116/13756) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitut e.org; dbSNP rs201869161). - |
OTOGL-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 19, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at