rs2034528
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378609.3(OTOGL):āc.6247A>Gā(p.Ile2083Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 1,505,062 control chromosomes in the GnomAD database, including 649,613 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 Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I2083T) has been classified as Uncertain significance.
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.6247A>G | p.Ile2083Val | missense_variant | 52/59 | ENST00000547103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.6247A>G | p.Ile2083Val | missense_variant | 52/59 | 5 | NM_001378609.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.942 AC: 143322AN: 152162Hom.: 67568 Cov.: 32
GnomAD3 exomes AF: 0.941 AC: 139151AN: 147890Hom.: 65523 AF XY: 0.939 AC XY: 73229AN XY: 77972
GnomAD4 exome AF: 0.927 AC: 1254466AN: 1352782Hom.: 582006 Cov.: 34 AF XY: 0.927 AC XY: 620823AN XY: 669428
GnomAD4 genome ? AF: 0.942 AC: 143416AN: 152280Hom.: 67607 Cov.: 32 AF XY: 0.944 AC XY: 70315AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 11, 2015 | Ile2074Val in exon 51 of OTOGL: This variant is not expected to have clinical si gnificance because it has been identified in 7.6% (641/8456) of European America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs2034528). - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at