Variant 17-15314120-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031898.3(TEKT3):c.845G>C(p.Gly282Ala) variant causes a missense change. The variant allele was found at a frequency of 0.479 in 1,613,942 control chromosomes in the GnomAD database, including 187,679 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.43 ( 14619 hom., cov: 33)

Exomes 𝑓: 0.48 ( 173060 hom. )

Consequence

TEKT3
NM_031898.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.86

Variant links:

Genes affected

TEKT3 (HGNC:14293): (tektin 3) This gene product belongs to the tektin family of proteins. Tektins comprise a family of filament-forming proteins that are coassembled with tubulins to form ciliary and flagellar microtubules. The exact function of this gene is not known. [provided by RefSeq, Jul 2008]

TEKT3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004557818).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEKT3	NM_031898.3 linkuse as main transcript	c.845G>C	p.Gly282Ala	missense_variant	6/9	ENST00000395930.6	NP_114104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TEKT3	ENST00000395930.6 linkuse as main transcript	c.845G>C	p.Gly282Ala	missense_variant	6/9	1	NM_031898.3	ENSP00000379263	P1
TEKT3	ENST00000338696.6 linkuse as main transcript	c.845G>C	p.Gly282Ala	missense_variant	4/7	1		ENSP00000343995	P1
TEKT3	ENST00000539245.5 linkuse as main transcript	c.347G>C	p.Gly116Ala	missense_variant	7/8	5		ENSP00000443280
TEKT3	ENST00000395931.6 linkuse as main transcript	c.*145G>C		3_prime_UTR_variant, NMD_transcript_variant	4/8	5		ENSP00000379264

Frequencies

GnomAD3 genomes

AF:

0.431

AC:

65492

AN:

151992

Hom.:

14613

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.433

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.518

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.484

Gnomad OTH

AF:

0.421

GnomAD3 exomes

AF:

0.456

AC:

114664

AN:

251388

Hom.:

26716

AF XY:

0.464

AC XY:

63072

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.318

Gnomad AMR exome

AF:

0.389

Gnomad ASJ exome

AF:

0.395

Gnomad EAS exome

AF:

0.435

Gnomad SAS exome

AF:

0.520

Gnomad FIN exome

AF:

0.509

Gnomad NFE exome

AF:

0.478

Gnomad OTH exome

AF:

0.449

GnomAD4 exome

AF:

0.484

AC:

706938

AN:

1461832

Hom.:

173060

Cov.:

AF XY:

0.485

AC XY:

352625

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.311

Gnomad4 AMR exome

AF:

0.394

Gnomad4 ASJ exome

AF:

0.397

Gnomad4 EAS exome

AF:

0.413

Gnomad4 SAS exome

AF:

0.519

Gnomad4 FIN exome

AF:

0.503

Gnomad4 NFE exome

AF:

0.495

Gnomad4 OTH exome

AF:

0.470

GnomAD4 genome

AF:

0.431

AC:

65524

AN:

152110

Hom.:

14619

Cov.:

AF XY:

0.431

AC XY:

32050

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.322

Gnomad4 AMR

AF:

0.407

Gnomad4 ASJ

AF:

0.400

Gnomad4 EAS

AF:

0.434

Gnomad4 SAS

AF:

0.525

Gnomad4 FIN

AF:

0.518

Gnomad4 NFE

AF:

0.484

Gnomad4 OTH

AF:

0.420

Alfa

AF:

0.455

Hom.:

11970

Bravo

AF:

0.416

TwinsUK

AF:

0.476

AC:

1765

ALSPAC

AF:

0.494

AC:

1902

ESP6500AA

AF:

0.326

AC:

1437

ESP6500EA

AF:

0.481

AC:

4137

ExAC

AF:

0.457

AC:

55433

Asia WGS

AF:

0.428

AC:

1491

AN:

3478

EpiCase

AF:

0.466

EpiControl

AF:

0.460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Benign

0.94

DEOGEN2

Benign

0.015

T;T;T

Eigen

Benign

-0.22

Eigen_PC

Benign

-0.041

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.59

.;T;T

MetaRNN

Benign

0.0046

T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

2.0

M;M;.

MutationTaster

Benign

0.13

P;P

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.51

N;N;N

REVEL

Benign

0.099

Sift

Benign

0.15

T;T;T

Sift4G

Benign

0.76

T;T;.

Polyphen

0.0010

B;B;.

Vest4

0.14

MPC

0.17

ClinPred

0.018

GERP RS

5.4

Varity_R

0.18

gMVP

0.46

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over