Variant rs2305959 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031898.3(TEKT3):c.579+92C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,310,438 control chromosomes in the GnomAD database, including 33,770 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 0.21 ( 3369 hom., cov: 32)

Exomes 𝑓: 0.23 ( 30401 hom. )

Consequence

TEKT3
NM_031898.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.276

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT3	NM_031898.3 linkuse as main transcript	c.579+92C>T		intron_variant		ENST00000395930.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT3	ENST00000395930.6 linkuse as main transcript	c.579+92C>T		intron_variant		1	NM_031898.3	P1

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31451

AN:

151954

Hom.:

3365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.252

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.218

GnomAD4 exome

AF:

0.227

AC:

263011

AN:

1158366

Hom.:

30401

AF XY:

0.227

AC XY:

129079

AN XY:

568124

show subpopulations

Gnomad4 AFR exome

AF:

0.160

Gnomad4 AMR exome

AF:

0.160

Gnomad4 ASJ exome

AF:

0.247

Gnomad4 EAS exome

AF:

0.260

Gnomad4 SAS exome

AF:

0.219

Gnomad4 FIN exome

AF:

0.202

Gnomad4 NFE exome

AF:

0.230

Gnomad4 OTH exome

AF:

0.227

GnomAD4 genome

AF:

0.207

AC:

31469

AN:

152072

Hom.:

3369

Cov.:

AF XY:

0.206

AC XY:

15334

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.169

Gnomad4 ASJ

AF:

0.257

Gnomad4 EAS

AF:

0.252

Gnomad4 SAS

AF:

0.224

Gnomad4 FIN

AF:

0.189

Gnomad4 NFE

AF:

0.237

Gnomad4 OTH

AF:

0.219

Alfa

AF:

0.235

Hom.:

4149

Bravo

AF:

0.205

Asia WGS

AF:

0.228

AC:

790

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.46

DANN

Benign

0.31

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

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