Variant rs17804647 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_053285.2(TEKT1):c.1044C>T(p.Val348=) 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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TEKT1	NM_053285.2 linkuse as main transcript	c.1044C>T	p.Val348=	synonymous_variant	7/8	ENST00000338694.7	NP_444515.1
TEKT1	XM_011524027.4 linkuse as main transcript	c.853-518C>T		intron_variant			XP_011522329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TEKT1	ENST00000338694.7 linkuse as main transcript	c.1044C>T	p.Val348=	synonymous_variant	7/8	1	NM_053285.2	ENSP00000341346	P1
TEKT1	ENST00000571744.1 linkuse as main transcript	c.187-11422C>T		intron_variant		3		ENSP00000460197
TEKT1	ENST00000572291.1 linkuse as main transcript	c.239-518C>T		intron_variant		5		ENSP00000458518
TEKT1	ENST00000575592.1 linkuse as main transcript	c.*635C>T		3_prime_UTR_variant, NMD_transcript_variant	6/7	2		ENSP00000460359

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

GnomAD3 exomes

AF:

0.0858

AC:

21286

AN:

248182

Hom.:

1161

AF XY:

0.0879

AC XY:

11786

AN XY:

134102

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 SAS exome

AF:

0.0588

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

Gnomad4 AFR exome

AF:

0.0546

Gnomad4 AMR exome

AF:

0.0625

Gnomad4 ASJ exome

AF:

0.134

Gnomad4 EAS exome

AF:

0.000480

Gnomad4 SAS exome

AF:

0.0596

Gnomad4 FIN exome

AF:

0.104

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.0884

AC:

13447

AN:

152118

Hom.:

702

Cov.:

AF XY:

0.0882

AC XY:

6559

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0539

Gnomad4 AMR

AF:

0.0969

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.00155

Gnomad4 SAS

AF:

0.0521

Gnomad4 FIN

AF:

0.107

Gnomad4 NFE

AF:

0.109

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.107

Hom.:

1573

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

DANN

Benign

0.76

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over