Genetic Variant NM_031898.3: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKT3	NM_031898.3 link	c.664-72dupT		intron_variant	Intron 4 of 8	ENST00000395930.6	NP_114104.1	Q9BXF9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TEKT3	ENST00000395930.6 link	c.664-72_664-71insT	intron_variant	Intron 4 of 8	1	NM_031898.3	ENSP00000379263.1	Q9BXF9
TEKT3	ENST00000338696.6 link	c.664-72_664-71insT	intron_variant	Intron 2 of 6	1		ENSP00000343995.2	Q9BXF9
TEKT3	ENST00000539245.5 link	c.166-72_166-71insT	intron_variant	Intron 5 of 7	5		ENSP00000443280.1	F5H5M8
TEKT3	ENST00000395931.6 link	n.664-4940_664-4939insT	intron_variant	Intron 3 of 7	5		ENSP00000379264.2	J3KPT7

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 v4.3

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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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