rs76297160
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001378609.3(OTOGL):āc.1126A>Gā(p.Ile376Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00198 in 1,588,680 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
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.1126A>G | p.Ile376Val | missense_variant | 12/59 | ENST00000547103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.1126A>G | p.Ile376Val | missense_variant | 12/59 | 5 | NM_001378609.3 | P1 | |
OTOGL | ENST00000646859.1 | c.1126A>G | p.Ile376Val | missense_variant | 17/63 | ||||
OTOGL | ENST00000643417.1 | n.1786A>G | non_coding_transcript_exon_variant | 15/23 |
Frequencies
GnomAD3 genomes ? AF: 0.0104 AC: 1584AN: 152112Hom.: 29 Cov.: 32
GnomAD3 exomes AF: 0.00272 AC: 562AN: 206564Hom.: 13 AF XY: 0.00218 AC XY: 240AN XY: 110282
GnomAD4 exome AF: 0.00109 AC: 1562AN: 1436450Hom.: 32 Cov.: 30 AF XY: 0.000974 AC XY: 693AN XY: 711600
GnomAD4 genome ? AF: 0.0104 AC: 1589AN: 152230Hom.: 30 Cov.: 32 AF XY: 0.0100 AC XY: 748AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2014 | Ile367Val in exon 11 of OTOGL: This variant is not expected to have clinical sig nificance because it has been identified in 3.6% (135/3794) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs76297160). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 12, 2018 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at