rs9783425
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378609.3(OTOGL):c.2391-6G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,513,180 control chromosomes in the GnomAD database, including 1,321 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001378609.3 splice_region, splice_polypyrimidine_tract, intron
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.2391-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000547103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.2391-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001378609.3 | P1 | |||
OTOGL | ENST00000646859.1 | c.2391-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0542 AC: 8217AN: 151596Hom.: 716 Cov.: 31
GnomAD3 exomes AF: 0.0123 AC: 2279AN: 185720Hom.: 183 AF XY: 0.00934 AC XY: 928AN XY: 99372
GnomAD4 exome AF: 0.00543 AC: 7389AN: 1361472Hom.: 601 Cov.: 28 AF XY: 0.00467 AC XY: 3157AN XY: 676106
GnomAD4 genome ? AF: 0.0543 AC: 8235AN: 151708Hom.: 720 Cov.: 31 AF XY: 0.0516 AC XY: 3824AN XY: 74112
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 | 2364-6G>A in intron 20 of OTOGL: This variant is not expected to have clinical s ignificance because it has been identified in 18.5% (678/3662) of African Americ an chromosomes from a broad population by the NHLBI Exome Sequencing Project (ht tp://evs.gs.washington.edu/EVS; dbSNP rs9783425). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 17, 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. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 23, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at