Variant 17-6812865-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The ENST00000338694.7(TEKT1):c.818A>G(p.Asp273Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00178 in 1,614,092 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0011 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0018 ( 4 hom. )

Consequence

TEKT1
ENST00000338694.7 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.619

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 -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.010000646).

BP6

Variant 17-6812865-T-C is Benign according to our data. Variant chr17-6812865-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3038118.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEKT1	NM_053285.2 linkuse as main transcript	c.818A>G	p.Asp273Gly	missense_variant	6/8	ENST00000338694.7	NP_444515.1
TEKT1	XM_011524027.4 linkuse as main transcript	c.818A>G	p.Asp273Gly	missense_variant	6/7		XP_011522329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TEKT1	ENST00000338694.7 linkuse as main transcript	c.818A>G	p.Asp273Gly	missense_variant	6/8	1	NM_053285.2	ENSP00000341346	P1
TEKT1	ENST00000572291.1 linkuse as main transcript	c.206A>G	p.Asp69Gly	missense_variant	2/3	5		ENSP00000458518
TEKT1	ENST00000571744.1 linkuse as main transcript	c.152A>G	p.Asp51Gly	missense_variant	1/2	3		ENSP00000460197
TEKT1	ENST00000575592.1 linkuse as main transcript	c.*409A>G		3_prime_UTR_variant, NMD_transcript_variant	5/7	2		ENSP00000460359

Frequencies

GnomAD3 genomes

AF:

0.00115

AC:

175

AN:

152240

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000314

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00245

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00198

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00126

AC:

317

AN:

251304

Hom.:

AF XY:

0.00120

AC XY:

163

AN XY:

135812

show subpopulations

Gnomad AFR exome

AF:

0.000308

Gnomad AMR exome

AF:

0.000231

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00273

Gnomad NFE exome

AF:

0.00209

Gnomad OTH exome

AF:

0.00131

GnomAD4 exome

AF:

0.00185

AC:

2698

AN:

1461734

Hom.:

Cov.:

AF XY:

0.00173

AC XY:

1257

AN XY:

727154

show subpopulations

Gnomad4 AFR exome

AF:

0.000388

Gnomad4 AMR exome

AF:

0.000246

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00351

Gnomad4 NFE exome

AF:

0.00212

Gnomad4 OTH exome

AF:

0.00212

GnomAD4 genome

AF:

0.00115

AC:

175

AN:

152358

Hom.:

Cov.:

AF XY:

0.00105

AC XY:

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.000313

Gnomad4 AMR

AF:

0.0000653

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00245

Gnomad4 NFE

AF:

0.00198

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00167

Hom.:

Bravo

AF:

0.000933

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00130

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00174

AC:

ExAC

AF:

0.00139

AC:

169

EpiCase

AF:

0.00196

EpiControl

AF:

0.00107

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TEKT1-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 02, 2022

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.012

T;T

Eigen

Benign

-0.71

Eigen_PC

Benign

-0.66

FATHMM_MKL

Benign

0.67

LIST_S2

Benign

0.51

T;T

M_CAP

Benign

0.015

MetaRNN

Benign

0.010

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Uncertain

2.4

.;M

MutationTaster

Benign

0.89

D;D

PrimateAI

Benign

0.31

PROVEAN

Uncertain

-3.5

.;D

REVEL

Benign

0.13

Sift

Benign

0.094

.;T

Sift4G

Benign

0.21

T;T

Polyphen

0.015

.;B

Vest4

0.22

MVP

0.20

MPC

0.11

ClinPred

0.025

GERP RS

-1.2

Varity_R

0.20

gMVP

0.34

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over