Variant 10-112293788-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_058222.3(TECTB):c.534C>G(p.Ser178=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,613,384 control chromosomes in the GnomAD database, including 193,549 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.51 ( 20412 hom., cov: 32)

Exomes 𝑓: 0.48 ( 173137 hom. )

Consequence

TECTB
NM_058222.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -3.02

Variant links:

Genes affected

TECTB (HGNC:11721): (tectorin beta) This gene encodes a non-collagenous glycoprotein component of the tectorial membrane, which covers the auditory hair cells in the cochlea of the inner ear. A similar protein in mouse functions in low-frequency hearing. [provided by RefSeq, Jul 2013]

TECTB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 10-112293788-C-G is Benign according to our data. Variant chr10-112293788-C-G is described in ClinVar as [Benign]. Clinvar id is 3059723.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-112293788-C-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-3.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TECTB	NM_058222.3 linkuse as main transcript	c.534C>G	p.Ser178=	synonymous_variant	6/11	ENST00000646139.2	NP_478129.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TECTB	ENST00000646139.2 linkuse as main transcript	c.534C>G	p.Ser178=	synonymous_variant	6/11		NM_058222.3	ENSP00000494896	P1
TECTB	ENST00000369422.4 linkuse as main transcript	c.534C>G	p.Ser178=	synonymous_variant	5/10	1		ENSP00000358430	P1
TECTB	ENST00000643850.1 linkuse as main transcript	c.564C>G	p.Ser188=	synonymous_variant	6/11			ENSP00000495832
TECTB	ENST00000645243.1 linkuse as main transcript	c.534C>G	p.Ser178=	synonymous_variant	6/11			ENSP00000495514

Frequencies

GnomAD3 genomes

AF:

0.511

AC:

77636

AN:

151830

Hom.:

20374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.567

Gnomad AMI

AF:

0.521

Gnomad AMR

AF:

0.602

Gnomad ASJ

AF:

0.446

Gnomad EAS

AF:

0.743

Gnomad SAS

AF:

0.563

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.490

Gnomad NFE

AF:

0.463

Gnomad OTH

AF:

0.507

GnomAD3 exomes

AF:

0.527

AC:

132501

AN:

251448

Hom.:

36662

AF XY:

0.520

AC XY:

70656

AN XY:

135906

show subpopulations

Gnomad AFR exome

AF:

0.561

Gnomad AMR exome

AF:

0.704

Gnomad ASJ exome

AF:

0.423

Gnomad EAS exome

AF:

0.739

Gnomad SAS exome

AF:

0.570

Gnomad FIN exome

AF:

0.373

Gnomad NFE exome

AF:

0.463

Gnomad OTH exome

AF:

0.482

GnomAD4 exome

AF:

0.481

AC:

702787

AN:

1461436

Hom.:

173137

Cov.:

AF XY:

0.483

AC XY:

351085

AN XY:

727058

show subpopulations

Gnomad4 AFR exome

AF:

0.558

Gnomad4 AMR exome

AF:

0.690

Gnomad4 ASJ exome

AF:

0.431

Gnomad4 EAS exome

AF:

0.745

Gnomad4 SAS exome

AF:

0.566

Gnomad4 FIN exome

AF:

0.382

Gnomad4 NFE exome

AF:

0.459

Gnomad4 OTH exome

AF:

0.493

GnomAD4 genome

AF:

0.512

AC:

77730

AN:

151948

Hom.:

20412

Cov.:

AF XY:

0.513

AC XY:

38104

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.567

Gnomad4 AMR

AF:

0.603

Gnomad4 ASJ

AF:

0.446

Gnomad4 EAS

AF:

0.744

Gnomad4 SAS

AF:

0.564

Gnomad4 FIN

AF:

0.360

Gnomad4 NFE

AF:

0.463

Gnomad4 OTH

AF:

0.512

Alfa

AF:

0.393

Hom.:

1789

Bravo

AF:

0.531

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TECTB-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 20, 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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.24

DANN

Benign

0.54

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