Variant 10-112284664-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_058222.3(TECTB):c.206A>T(p.Tyr69Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000116 in 1,460,906 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.000012 ( 1 hom. )

Consequence

TECTB
NM_058222.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.59

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.40871793).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TECTB	NM_058222.3 linkuse as main transcript	c.206A>T	p.Tyr69Phe	missense_variant	3/11	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.206A>T	p.Tyr69Phe	missense_variant	3/11		NM_058222.3	ENSP00000494896	P1
TECTB	ENST00000369422.4 linkuse as main transcript	c.206A>T	p.Tyr69Phe	missense_variant	2/10	1		ENSP00000358430	P1
TECTB	ENST00000643850.1 linkuse as main transcript	c.206A>T	p.Tyr69Phe	missense_variant	3/11			ENSP00000495832
TECTB	ENST00000645243.1 linkuse as main transcript	c.206A>T	p.Tyr69Phe	missense_variant	3/11			ENSP00000495514

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000200

AC:

AN:

250144

Hom.:

AF XY:

0.0000296

AC XY:

AN XY:

135182

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000165

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000116

AC:

AN:

1460906

Hom.:

Cov.:

AF XY:

0.0000165

AC XY:

AN XY:

726684

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000186

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

Cov.:

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 20, 2021

The c.206A>T (p.Y69F) alteration is located in exon 2 (coding exon 2) of the TECTB gene. This alteration results from a A to T substitution at nucleotide position 206, causing the tyrosine (Y) at amino acid position 69 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Benign

-0.14

CADD

Uncertain

DANN

Benign

0.97

DEOGEN2

Benign

0.27

.;T;.;T

Eigen

Uncertain

0.57

Eigen_PC

Uncertain

0.59

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.90

D;.;D;D

M_CAP

Uncertain

0.14

MetaRNN

Benign

0.41

T;T;T;T

MetaSVM

Uncertain

0.013

MutationAssessor

Benign

1.4

.;L;.;L

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.69

PROVEAN

Benign

-0.95

.;.;.;N

REVEL

Uncertain

0.42

Sift

Benign

1.0

.;.;.;T

Sift4G

Pathogenic

0.0

.;.;.;D

Polyphen

1.0

.;D;.;D

Vest4

0.43

MutPred

0.60

Loss of phosphorylation at Y69 (P = 0.0647);Loss of phosphorylation at Y69 (P = 0.0647);Loss of phosphorylation at Y69 (P = 0.0647);Loss of phosphorylation at Y69 (P = 0.0647);

MVP

0.57

MPC

0.28

ClinPred

0.57

GERP RS

5.8

Varity_R

0.24

gMVP

0.58

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