Genetic Variant TEKT3:c.663+43T>C (chr17-15327949-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031898.3(TEKT3):c.663+43T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,553,806 control chromosomes in the GnomAD database, including 10,286 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 0.098 ( 861 hom., cov: 33)

Exomes 𝑓: 0.11 ( 9425 hom. )

Consequence

TEKT3
NM_031898.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0710

Publications

5 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKT3	NM_031898.3 link	c.663+43T>C		intron_variant	Intron 4 of 8	ENST00000395930.6	NP_114104.1	Q9BXF9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEKT3	ENST00000395930.6 link	c.663+43T>C		intron_variant	Intron 4 of 8	1	NM_031898.3	ENSP00000379263.1		Q9BXF9

Frequencies

GnomAD3 genomes

AF:

0.0979

AC:

14900

AN:

152140

Hom.:

862

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0518

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.218

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.105

Gnomad OTH

AF:

0.0923

GnomAD2 exomes

AF:

0.122

AC:

30649

AN:

250582

AF XY:

0.122

show subpopulations

Gnomad AFR exome

AF:

0.0506

Gnomad AMR exome

AF:

0.169

Gnomad ASJ exome

AF:

0.0939

Gnomad EAS exome

AF:

0.220

Gnomad FIN exome

AF:

0.103

Gnomad NFE exome

AF:

0.103

Gnomad OTH exome

AF:

0.107

GnomAD4 exome

AF:

0.111

AC:

155456

AN:

1401548

Hom.:

9425

Cov.:

AF XY:

0.112

AC XY:

78140

AN XY:

700074

show subpopulations

African (AFR)

AF:

0.0497

AC:

1605

AN:

32280

American (AMR)

AF:

0.165

AC:

7366

AN:

44564

Ashkenazi Jewish (ASJ)

AF:

0.0915

AC:

2359

AN:

25768

East Asian (EAS)

AF:

0.206

AC:

8086

AN:

39268

South Asian (SAS)

AF:

0.146

AC:

12385

AN:

84776

European-Finnish (FIN)

AF:

0.104

AC:

5519

AN:

53172

Middle Eastern (MID)

AF:

0.0608

AC:

343

AN:

5644

European-Non Finnish (NFE)

AF:

0.105

AC:

111566

AN:

1057686

Other (OTH)

AF:

0.107

AC:

6227

AN:

58390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

6653

13306

19960

26613

33266

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4190

8380

12570

16760

20950

<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:

0.0979

AC:

14912

AN:

152258

Hom.:

861

Cov.:

AF XY:

0.0985

AC XY:

7333

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.0521

AC:

2167

AN:

41572

American (AMR)

AF:

0.132

AC:

2019

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

352

AN:

3470

East Asian (EAS)

AF:

0.218

AC:

1127

AN:

5178

South Asian (SAS)

AF:

0.157

AC:

754

AN:

4814

European-Finnish (FIN)

AF:

0.102

AC:

1086

AN:

10600

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.105

AC:

7151

AN:

68008

Other (OTH)

AF:

0.0903

AC:

191

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

682

1365

2047

2730

3412

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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:

0.0979

Hom.:

255

Bravo

AF:

0.0983

Asia WGS

AF:

0.189

AC:

659

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.9

(source)

DANN

Benign

0.57

PhyloP100

0.071

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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