rs145689709
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001292063.2(OTOG):c.4022G>A(p.Arg1341Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00349 in 1,550,594 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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_001292063.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.4022G>A | p.Arg1341Gln | missense_variant | Exon 33 of 56 | 5 | NM_001292063.2 | ENSP00000382329.2 | ||
OTOG | ENST00000399391.7 | c.4058G>A | p.Arg1353Gln | missense_variant | Exon 32 of 55 | 5 | ENSP00000382323.2 | |||
OTOG | ENST00000342528.2 | n.1360G>A | non_coding_transcript_exon_variant | Exon 9 of 22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00284 AC: 433AN: 152228Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00242 AC: 360AN: 148718Hom.: 0 AF XY: 0.00255 AC XY: 204AN XY: 80130
GnomAD4 exome AF: 0.00356 AC: 4974AN: 1398248Hom.: 16 Cov.: 30 AF XY: 0.00345 AC XY: 2379AN XY: 689654
GnomAD4 genome AF: 0.00283 AC: 431AN: 152346Hom.: 1 Cov.: 33 AF XY: 0.00252 AC XY: 188AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:3
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OTOG: BP4, BS2 -
Meniere disease Uncertain:1
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not specified Benign:1
p.Arg1353Gln in exon 32 of OTOG: This variant is not expected to have clinical s ignificance because it has been identified in 0.56% (29/5214) of European chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs145689709). -
OTOG-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at