dbSNP rs2286516: TEKT3:p.Gln339Gln (chr17-15312343-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_031898.3(TEKT3):c.1017A>G(p.Gln339Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,613,950 control chromosomes in the GnomAD database, including 55,434 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.24 ( 4670 hom., cov: 33)

Exomes 𝑓: 0.26 ( 50764 hom. )

Consequence

TEKT3
NM_031898.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.648

Publications

16 publications found

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 Gene-Disease associations (from GenCC):

spermatogenic failure 81
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

TEKT3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP7

Synonymous conserved (PhyloP=0.648 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKT3	NM_031898.3 link	c.1017A>G	p.Gln339Gln	synonymous_variant	Exon 7 of 9	ENST00000395930.6	NP_114104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEKT3	ENST00000395930.6 link	c.1017A>G	p.Gln339Gln	synonymous_variant	Exon 7 of 9	1	NM_031898.3	ENSP00000379263.1

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36505

AN:

152078

Hom.:

4667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.250

GnomAD2 exomes

AF:

0.273

AC:

68590

AN:

251434

AF XY:

0.273

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.328

Gnomad ASJ exome

AF:

0.326

Gnomad EAS exome

AF:

0.256

Gnomad FIN exome

AF:

0.282

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.271

GnomAD4 exome

AF:

0.261

AC:

381614

AN:

1461754

Hom.:

50764

Cov.:

AF XY:

0.262

AC XY:

190418

AN XY:

727176

show subpopulations

African (AFR)

AF:

0.160

AC:

5355

AN:

33478

American (AMR)

AF:

0.318

AC:

14216

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.327

AC:

8541

AN:

26136

East Asian (EAS)

AF:

0.272

AC:

10794

AN:

39700

South Asian (SAS)

AF:

0.277

AC:

23921

AN:

86252

European-Finnish (FIN)

AF:

0.287

AC:

15348

AN:

53414

Middle Eastern (MID)

AF:

0.324

AC:

1870

AN:

5768

European-Non Finnish (NFE)

AF:

0.257

AC:

286109

AN:

1111886

Other (OTH)

AF:

0.256

AC:

15460

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

16540

33079

49619

66158

82698

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9702

19404

29106

38808

48510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.240

AC:

36508

AN:

152196

Hom.:

4670

Cov.:

AF XY:

0.242

AC XY:

18029

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.163

AC:

6765

AN:

41542

American (AMR)

AF:

0.287

AC:

4386

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1105

AN:

3470

East Asian (EAS)

AF:

0.265

AC:

1375

AN:

5192

South Asian (SAS)

AF:

0.264

AC:

1272

AN:

4826

European-Finnish (FIN)

AF:

0.286

AC:

3020

AN:

10574

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.259

AC:

17610

AN:

67986

Other (OTH)

AF:

0.252

AC:

532

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1401

2802

4204

5605

7006

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.260

Hom.:

10345

Bravo

AF:

0.237

Asia WGS

AF:

0.308

AC:

1072

AN:

3478

EpiCase

AF:

0.267

EpiControl

AF:

0.277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

4.4

(source)

DANN

Benign

0.64

PhyloP100

0.65

Mutation Taster

=92/8

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over