dbSNP rs2305959: TEKT3:c.579+92C>T (chr17-15330915-G-A) – 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.579+92C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,310,438 control chromosomes in the GnomAD database, including 33,770 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 0.21 ( 3369 hom., cov: 32)

Exomes 𝑓: 0.23 ( 30401 hom. )

Consequence

TEKT3
NM_031898.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.276

Publications

3 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKT3	NM_031898.3 link	c.579+92C>T		intron_variant	Intron 3 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.579+92C>T		intron_variant	Intron 3 of 8	1	NM_031898.3	ENSP00000379263.1		Q9BXF9

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31451

AN:

151954

Hom.:

3365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.252

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.218

GnomAD4 exome

AF:

0.227

AC:

263011

AN:

1158366

Hom.:

30401

AF XY:

0.227

AC XY:

129079

AN XY:

568124

show subpopulations

African (AFR)

AF:

0.160

AC:

4104

AN:

25578

American (AMR)

AF:

0.160

AC:

3133

AN:

19596

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

4483

AN:

18124

East Asian (EAS)

AF:

0.260

AC:

8984

AN:

34492

South Asian (SAS)

AF:

0.219

AC:

12934

AN:

59092

European-Finnish (FIN)

AF:

0.202

AC:

8213

AN:

40738

Middle Eastern (MID)

AF:

0.247

AC:

1202

AN:

4866

European-Non Finnish (NFE)

AF:

0.230

AC:

208773

AN:

906684

Other (OTH)

AF:

0.227

AC:

11185

AN:

49196

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

10109

20217

30326

40434

50543

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7112

14224

21336

28448

35560

<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:

0.207

AC:

31469

AN:

152072

Hom.:

3369

Cov.:

AF XY:

0.206

AC XY:

15334

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.164

AC:

6800

AN:

41472

American (AMR)

AF:

0.169

AC:

2577

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

890

AN:

3468

East Asian (EAS)

AF:

0.252

AC:

1306

AN:

5178

South Asian (SAS)

AF:

0.224

AC:

1079

AN:

4818

European-Finnish (FIN)

AF:

0.189

AC:

1998

AN:

10558

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.237

AC:

16132

AN:

67972

Other (OTH)

AF:

0.219

AC:

463

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1297

2593

3890

5186

6483

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<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:

0.230

Hom.:

5271

Bravo

AF:

0.205

Asia WGS

AF:

0.228

AC:

790

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.46

(source)

DANN

Benign

0.31

PhyloP100

-0.28

Mutation Taster

=100/0

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