dbSNP rs8078571: TEKT1:p.Pro8Pro (chr17-6830353-T-C) – 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.24A>G(p.Pro8Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 1,591,900 control chromosomes in the GnomAD database, including 194,267 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 0.57 ( 26555 hom., cov: 32)

Exomes 𝑓: 0.48 ( 167712 hom. )

Consequence

TEKT1
NM_053285.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.77

Publications

25 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=-0.85).

BP7

Synonymous conserved (PhyloP=-1.77 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKT1	NM_053285.2 link	c.24A>G	p.Pro8Pro	synonymous_variant	Exon 2 of 8	ENST00000338694.7	NP_444515.1	Q969V4
TEKT1	XM_011524027.4 link	c.24A>G	p.Pro8Pro	synonymous_variant	Exon 2 of 7		XP_011522329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TEKT1	ENST00000338694.7 link	c.24A>G	p.Pro8Pro	synonymous_variant	Exon 2 of 8	1	NM_053285.2	ENSP00000341346.2	Q969V4
TEKT1	ENST00000573966.1 link	n.151A>G		non_coding_transcript_exon_variant	Exon 2 of 4	3
TEKT1	ENST00000575592.1 link	n.24A>G		non_coding_transcript_exon_variant	Exon 2 of 7	2		ENSP00000460359.1	I3L3D4

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

86214

AN:

151996

Hom.:

26505

Cov.:

show subpopulations

Gnomad AFR

AF:

0.829

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.449

Gnomad ASJ

AF:

0.439

Gnomad EAS

AF:

0.546

Gnomad SAS

AF:

0.511

Gnomad FIN

AF:

0.456

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.466

Gnomad OTH

AF:

0.522

GnomAD2 exomes

AF:

0.495

AC:

113939

AN:

230082

AF XY:

0.487

show subpopulations

Gnomad AFR exome

AF:

0.843

Gnomad AMR exome

AF:

0.421

Gnomad ASJ exome

AF:

0.441

Gnomad EAS exome

AF:

0.559

Gnomad FIN exome

AF:

0.464

Gnomad NFE exome

AF:

0.466

Gnomad OTH exome

AF:

0.466

GnomAD4 exome

AF:

0.478

AC:

688521

AN:

1439786

Hom.:

167712

Cov.:

AF XY:

0.476

AC XY:

340982

AN XY:

715848

show subpopulations

African (AFR)

AF:

0.847

AC:

27265

AN:

32188

American (AMR)

AF:

0.421

AC:

15687

AN:

37294

Ashkenazi Jewish (ASJ)

AF:

0.441

AC:

11239

AN:

25480

East Asian (EAS)

AF:

0.568

AC:

22205

AN:

39070

South Asian (SAS)

AF:

0.488

AC:

39616

AN:

81118

European-Finnish (FIN)

AF:

0.476

AC:

25363

AN:

53290

Middle Eastern (MID)

AF:

0.416

AC:

2371

AN:

5706

European-Non Finnish (NFE)

AF:

0.466

AC:

515297

AN:

1106224

Other (OTH)

AF:

0.496

AC:

29478

AN:

59416

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

16191

32382

48573

64764

80955

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15550

31100

46650

62200

77750

<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:

0.567

AC:

86310

AN:

152114

Hom.:

26555

Cov.:

AF XY:

0.562

AC XY:

41789

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.830

AC:

34442

AN:

41520

American (AMR)

AF:

0.449

AC:

6854

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.439

AC:

1524

AN:

3470

East Asian (EAS)

AF:

0.546

AC:

2823

AN:

5166

South Asian (SAS)

AF:

0.510

AC:

2460

AN:

4822

European-Finnish (FIN)

AF:

0.456

AC:

4822

AN:

10572

Middle Eastern (MID)

AF:

0.500

AC:

147

AN:

294

European-Non Finnish (NFE)

AF:

0.466

AC:

31703

AN:

67968

Other (OTH)

AF:

0.521

AC:

1098

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1717

3434

5150

6867

8584

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.495

Hom.:

91323

Bravo

AF:

0.578

Asia WGS

AF:

0.549

AC:

1911

AN:

3478

EpiCase

AF:

0.465

EpiControl

AF:

0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.23

(source)

DANN

Benign

0.48

PhyloP100

-1.8

Mutation Taster

=300/0

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