rs201877625
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001378609.3(OTOGL):c.6782-3C>T 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 0.00134 in 1,596,548 control chromosomes in the GnomAD database, including 48 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 -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOGL | NM_001378609.3 | c.6782-3C>T | 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.6782-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001378609.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000731 AC: 111AN: 151838Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00293 AC: 714AN: 243594Hom.: 12 AF XY: 0.00400 AC XY: 528AN XY: 131864
GnomAD4 exome AF: 0.00140 AC: 2027AN: 1444592Hom.: 47 Cov.: 29 AF XY: 0.00206 AC XY: 1480AN XY: 718554
GnomAD4 genome ? AF: 0.000724 AC: 110AN: 151956Hom.: 1 Cov.: 33 AF XY: 0.00113 AC XY: 84AN XY: 74232
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 26, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 01, 2015 | c.6755-3C>T in intron 56 of OTOGL: This variant is not expected to have clinical significance because it has been identified in 2.3% (357/15826) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitut e.org; dbSNP rs201877625). - |
OTOGL-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 15, 2019 | This variant is classified as 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