rs367996419

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1

The NM_001378609.3(OTOGL):​c.1441+10T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000849 in 1,599,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.00062 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00087 ( 0 hom. )

Consequence

OTOGL
NM_001378609.3 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.154
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 12-80254580-T-A is Benign according to our data. Variant chr12-80254580-T-A is described in ClinVar as [Benign]. Clinvar id is 227811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-80254580-T-A is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.000874 (1264/1446948) while in subpopulation AMR AF= 0.0038 (169/44474). AF 95% confidence interval is 0.00333. There are 0 homozygotes in gnomad4_exome. There are 613 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OTOGLNM_001378609.3 linkuse as main transcriptc.1441+10T>A intron_variant ENST00000547103.7 NP_001365538.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OTOGLENST00000547103.7 linkuse as main transcriptc.1441+10T>A intron_variant 5 NM_001378609.3 ENSP00000447211 P1
OTOGLENST00000646859.1 linkuse as main transcriptc.1441+10T>A intron_variant ENSP00000496036
OTOGLENST00000643417.1 linkuse as main transcriptn.2101+10T>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.000619
AC:
94
AN:
151934
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000314
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00184
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00231
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000574
Gnomad OTH
AF:
0.000479
GnomAD3 exomes
AF:
0.000981
AC:
240
AN:
244652
Hom.:
0
AF XY:
0.000917
AC XY:
122
AN XY:
132980
show subpopulations
Gnomad AFR exome
AF:
0.000326
Gnomad AMR exome
AF:
0.00383
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00190
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000604
Gnomad OTH exome
AF:
0.000669
GnomAD4 exome
AF:
0.000874
AC:
1264
AN:
1446948
Hom.:
0
Cov.:
29
AF XY:
0.000851
AC XY:
613
AN XY:
720140
show subpopulations
Gnomad4 AFR exome
AF:
0.000271
Gnomad4 AMR exome
AF:
0.00380
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00228
Gnomad4 SAS exome
AF:
0.000106
Gnomad4 FIN exome
AF:
0.0000189
Gnomad4 NFE exome
AF:
0.000835
Gnomad4 OTH exome
AF:
0.00109
GnomAD4 genome
AF:
0.000618
AC:
94
AN:
152052
Hom.:
0
Cov.:
32
AF XY:
0.000673
AC XY:
50
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.000313
Gnomad4 AMR
AF:
0.00184
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00232
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000574
Gnomad4 OTH
AF:
0.000474
Alfa
AF:
0.000430
Hom.:
0
Bravo
AF:
0.000880
Asia WGS
AF:
0.000868
AC:
3
AN:
3470

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineJun 13, 2017c.1414+10T>A in intron 14 of OTOGL: This variant is not expected to have clinica l significance because it is not located within the splice consensus sequence. I t has been identified in 0.4% (131/34138) of Latino chromosomes by the Genome Ag gregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs367996419) . -
OTOGL-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesOct 31, 2019This 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). -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 11, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
0.30
DANN
Benign
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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.

Other links and lift over

dbSNP: rs367996419; hg19: chr12-80648360; API