Genetic Variant TEKT3:c.664-72dupT (chr17-15319218-C-CA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_031898.3(TEKT3):c.664-72dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 1,310,716 control chromosomes in the GnomAD database, including 250,176 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.65 ( 32486 hom., cov: 0)

Exomes 𝑓: 0.61 ( 217690 hom. )

Consequence

TEKT3
NM_031898.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0570

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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031898.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT3	NM_031898.3	MANE Select	c.664-72dupT		intron	N/A	NP_114104.1	Q9BXF9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TEKT3	ENST00000395930.6	TSL:1 MANE Select	c.664-72_664-71insT	intron	N/A	ENSP00000379263.1	Q9BXF9
TEKT3	ENST00000338696.6	TSL:1	c.664-72_664-71insT	intron	N/A	ENSP00000343995.2	Q9BXF9
TEKT3	ENST00000539245.5	TSL:5	c.166-72_166-71insT	intron	N/A	ENSP00000443280.1	F5H5M8

Frequencies

GnomAD3 genomes

AF:

0.651

AC:

98828

AN:

151922

Hom.:

32464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.722

Gnomad AMI

AF:

0.631

Gnomad AMR

AF:

0.691

Gnomad ASJ

AF:

0.686

Gnomad EAS

AF:

0.756

Gnomad SAS

AF:

0.648

Gnomad FIN

AF:

0.535

Gnomad MID

AF:

0.704

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.656

GnomAD4 exome

AF:

0.607

AC:

703369

AN:

1158676

Hom.:

217690

AF XY:

0.608

AC XY:

352191

AN XY:

579464

show subpopulations

African (AFR)

AF:

0.725

AC:

18609

AN:

25676

American (AMR)

AF:

0.715

AC:

18820

AN:

26340

Ashkenazi Jewish (ASJ)

AF:

0.675

AC:

14191

AN:

21022

East Asian (EAS)

AF:

0.765

AC:

28080

AN:

36692

South Asian (SAS)

AF:

0.639

AC:

41345

AN:

64706

European-Finnish (FIN)

AF:

0.544

AC:

27112

AN:

49834

Middle Eastern (MID)

AF:

0.667

AC:

2422

AN:

3630

European-Non Finnish (NFE)

AF:

0.593

AC:

522553

AN:

881624

Other (OTH)

AF:

0.615

AC:

30237

AN:

49152

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

12827

25654

38482

51309

64136

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13708

27416

41124

54832

68540

<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:

0.650

AC:

98899

AN:

152040

Hom.:

32486

Cov.:

AF XY:

0.650

AC XY:

48316

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.722

AC:

29935

AN:

41488

American (AMR)

AF:

0.691

AC:

10545

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.686

AC:

2379

AN:

3466

East Asian (EAS)

AF:

0.755

AC:

3917

AN:

5186

South Asian (SAS)

AF:

0.648

AC:

3122

AN:

4816

European-Finnish (FIN)

AF:

0.535

AC:

5646

AN:

10550

Middle Eastern (MID)

AF:

0.702

AC:

205

AN:

292

European-Non Finnish (NFE)

AF:

0.606

AC:

41192

AN:

67960

Other (OTH)

AF:

0.655

AC:

1384

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1775

3550

5324

7099

8874

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

790

1580

2370

3160

3950

<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:

0.617

Hom.:

3509

Bravo

AF:

0.666

Asia WGS

AF:

0.753

AC:

2617

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.057

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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17-15319218-CA-CAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over