rs149249642

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001378609.3(OTOGL):c.6283A>G(p.Ile2095Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000748 in 1,404,176 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0017 ( 1 hom., cov: 26)

Exomes 𝑓: 0.00063 ( 4 hom. )

Consequence

OTOGL
NM_001378609.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.545

Variant links:

Genes affected

OTOGL (HGNC:26901): (otogelin like) The protein encoded by this gene belongs to the otogelin family. This gene is expressed in the inner ear of vertebrates with the highest level of expression seen at the embryonic stage and lowest in adult. Knockdown studies in zebrafish suggest that this gene is essential for normal inner ear function. Mutations in this gene are associated with autosomal recessive deafness. [provided by RefSeq, Dec 2012]

OTOGL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008036017).

BP6

Variant 12-80366589-A-G is Benign according to our data. Variant chr12-80366589-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 226967.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-80366589-A-G is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00175 (259/148198) while in subpopulation AFR AF= 0.00391 (160/40882). AF 95% confidence interval is 0.00342. There are 1 homozygotes in gnomad4. There are 117 alleles in male gnomad4 subpopulation. Median coverage is 26. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OTOGL	NM_001378609.3 link	c.6283A>G	p.Ile2095Val	missense_variant	Exon 53 of 59	ENST00000547103.7	NP_001365538.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OTOGL	ENST00000547103.7 link	c.6283A>G	p.Ile2095Val	missense_variant	Exon 53 of 59	5	NM_001378609.3	ENSP00000447211.2		Q3ZCN5

Frequencies

GnomAD3 genomes

AF:

0.00175

AC:

259

AN:

148174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00390

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00272

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00662

Gnomad NFE

AF:

0.000713

Gnomad OTH

AF:

0.00440

GnomAD3 exomes

AF:

0.000905

AC:

157

AN:

173430

Hom.:

AF XY:

0.000842

AC XY:

AN XY:

96144

show subpopulations

Gnomad AFR exome

AF:

0.00389

Gnomad AMR exome

AF:

0.00161

Gnomad ASJ exome

AF:

0.000734

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000471

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000727

Gnomad OTH exome

AF:

0.00253

GnomAD4 exome

AF:

0.000631

AC:

792

AN:

1255978

Hom.:

Cov.:

AF XY:

0.000623

AC XY:

387

AN XY:

621326

show subpopulations

Gnomad4 AFR exome

AF:

0.00448

Gnomad4 AMR exome

AF:

0.00218

Gnomad4 ASJ exome

AF:

0.000424

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000372

Gnomad4 FIN exome

AF:

0.0000673

Gnomad4 NFE exome

AF:

0.000447

Gnomad4 OTH exome

AF:

0.00200

GnomAD4 genome

AF:

0.00175

AC:

259

AN:

148198

Hom.:

Cov.:

AF XY:

0.00162

AC XY:

117

AN XY:

72100

show subpopulations

Gnomad4 AFR

AF:

0.00391

Gnomad4 AMR

AF:

0.00265

Gnomad4 ASJ

AF:

0.000290

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000713

Gnomad4 OTH

AF:

0.00437

Alfa

AF:

0.000850

Hom.:

Bravo

AF:

0.00212

ESP6500AA

AF:

0.00273

AC:

ESP6500EA

AF:

0.000350

AC:

ExAC

AF:

0.000923

AC:

110

Asia WGS

AF:

0.00146

AC:

AN:

3446

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jan 07, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 12, 2021

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

Nov 24, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Ile2086Val in exon 52 of OTOGL: This variant is not expected to have clinical si gnificance because it has been identified in 4.6% (9/194) of Luhya (Kenyan) chro mosomes from a broad population by the 1000 Genomes Project (http://www.ncbi.nlm .nih.gov/projects/SNP; dbSNP rs149249642). -

OTOGL-related disorder

Benign:1

Jul 17, 2023

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.96

Eigen

Benign

-0.98

Eigen_PC

Benign

-0.97

FATHMM_MKL

Benign

0.24

LIST_S2

Benign

0.40

T;.;T

M_CAP

Benign

0.0030

MetaRNN

Benign

0.0080

T;T;T

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.67

.;.;N

REVEL

Benign

0.026

Sift

Benign

0.31

.;.;T

Sift4G

Benign

0.33

.;.;T

Vest4

0.13

MVP

0.030

MPC

0.021

ClinPred

0.0013

GERP RS

-1.6

gMVP

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over