Genetic Variant TEKT1:p.Val348Val (chr17-6800752-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_053285.2(TEKT1):c.1044C>T(p.Val348Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 1,610,346 control chromosomes in the GnomAD database, including 8,200 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 0.088 ( 702 hom., cov: 32)

Exomes 𝑓: 0.097 ( 7498 hom. )

Consequence

TEKT1
NM_053285.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.488

Publications

12 publications found

Variant links:

Genes affected

TEKT1 (HGNC:15534): (tektin 1) 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. This gene is predominantly expressed in the testis and in mouse, tektin 1 mRNA was localized to the spermatocytes and round spermatids in the seminiferous tubules, indicating that it may play a role in spermatogenesis. [provided by RefSeq, Jul 2008]

TEKT1 links:

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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=-0.83).

BP7

Synonymous conserved (PhyloP=-0.488 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKT1	NM_053285.2 link	c.1044C>T	p.Val348Val	synonymous_variant	Exon 7 of 8	ENST00000338694.7	NP_444515.1	Q969V4
TEKT1	XM_011524027.4 link	c.853-518C>T		intron_variant	Intron 6 of 6		XP_011522329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEKT1	ENST00000338694.7 link	c.1044C>T	p.Val348Val	synonymous_variant	Exon 7 of 8	1	NM_053285.2	ENSP00000341346.2		Q969V4

Frequencies

GnomAD3 genomes

AF:

0.0884

AC:

13437

AN:

152000

Hom.:

701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0537

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.0971

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.00155

Gnomad SAS

AF:

0.0523

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.104

GnomAD2 exomes

AF:

0.0858

AC:

21286

AN:

248182

AF XY:

0.0879

show subpopulations

Gnomad AFR exome

AF:

0.0485

Gnomad AMR exome

AF:

0.0579

Gnomad ASJ exome

AF:

0.138

Gnomad EAS exome

AF:

0.00120

Gnomad FIN exome

AF:

0.105

Gnomad NFE exome

AF:

0.111

Gnomad OTH exome

AF:

0.120

GnomAD4 exome

AF:

0.0966

AC:

140882

AN:

1458228

Hom.:

7498

Cov.:

AF XY:

0.0967

AC XY:

70101

AN XY:

724932

show subpopulations

African (AFR)

AF:

0.0546

AC:

1822

AN:

33396

American (AMR)

AF:

0.0625

AC:

2779

AN:

44452

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

3488

AN:

25968

East Asian (EAS)

AF:

0.000480

AC:

AN:

39612

South Asian (SAS)

AF:

0.0596

AC:

5110

AN:

85806

European-Finnish (FIN)

AF:

0.104

AC:

5526

AN:

53352

Middle Eastern (MID)

AF:

0.208

AC:

1184

AN:

5704

European-Non Finnish (NFE)

AF:

0.103

AC:

114698

AN:

1109706

Other (OTH)

AF:

0.104

AC:

6256

AN:

60232

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

6535

13070

19605

26140

32675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4024

8048

12072

16096

20120

<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:

0.0884

AC:

13447

AN:

152118

Hom.:

702

Cov.:

AF XY:

0.0882

AC XY:

6559

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0539

AC:

2238

AN:

41506

American (AMR)

AF:

0.0969

AC:

1481

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

513

AN:

3466

East Asian (EAS)

AF:

0.00155

AC:

AN:

5158

South Asian (SAS)

AF:

0.0521

AC:

251

AN:

4818

European-Finnish (FIN)

AF:

0.107

AC:

1130

AN:

10594

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.109

AC:

7412

AN:

67984

Other (OTH)

AF:

0.103

AC:

217

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

596

1192

1788

2384

2980

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.105

Hom.:

1855

Bravo

AF:

0.0866

Asia WGS

AF:

0.0340

AC:

117

AN:

3478

EpiCase

AF:

0.112

EpiControl

AF:

0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.1

(source)

DANN

Benign

0.76

PhyloP100

-0.49

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