Variant 12-80209626-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001378609.3(OTOGL):c.79+116A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 582,352 control chromosomes in the GnomAD database, including 66,525 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 14841 hom., cov: 32)

Exomes 𝑓: 0.48 ( 51684 hom. )

Consequence

OTOGL
NM_001378609.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.938

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:

OTOGL (HGNC:):

OTOGL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 12-80209626-A-T is Benign according to our data. Variant chr12-80209626-A-T is described in ClinVar as [Benign]. Clinvar id is 1274148.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OTOGL	NM_001378609.3 linkuse as main transcript	c.79+116A>T		intron_variant		ENST00000547103.7	NP_001365538.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
OTOGL	ENST00000547103.7 linkuse as main transcript	c.79+116A>T	intron_variant	5	NM_001378609.3	ENSP00000447211.2	Q3ZCN5
OTOGL	ENST00000646859.1 linkuse as main transcript	c.79+116A>T	intron_variant			ENSP00000496036.1	A0A2R8YF04
OTOGL	ENST00000643417.1 linkuse as main transcript	n.739+116A>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.404

AC:

61443

AN:

151910

Hom.:

14837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.427

Gnomad EAS

AF:

0.407

Gnomad SAS

AF:

0.511

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.515

Gnomad OTH

AF:

0.415

GnomAD4 exome

AF:

0.484

AC:

208173

AN:

430320

Hom.:

51684

AF XY:

0.486

AC XY:

109081

AN XY:

224556

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.613

Gnomad4 ASJ exome

AF:

0.423

Gnomad4 EAS exome

AF:

0.380

Gnomad4 SAS exome

AF:

0.513

Gnomad4 FIN exome

AF:

0.515

Gnomad4 NFE exome

AF:

0.502

Gnomad4 OTH exome

AF:

0.469

GnomAD4 genome

AF:

0.404

AC:

61454

AN:

152032

Hom.:

14841

Cov.:

AF XY:

0.407

AC XY:

30260

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.559

Gnomad4 ASJ

AF:

0.427

Gnomad4 EAS

AF:

0.407

Gnomad4 SAS

AF:

0.510

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.515

Gnomad4 OTH

AF:

0.414

Alfa

AF:

0.458

Hom.:

2175

Bravo

AF:

0.392

Asia WGS

AF:

0.461

AC:

1593

AN:

3450

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.94

DANN

Benign

0.78

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.

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