Genetic Variant NM_053285.2:c.1044C>T (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:

Genome browser will be placed here

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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