Variant 13-30968931-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_152325.3(TEX26):c.693G>T(p.Lys231Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00798 in 1,614,084 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0059 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0082 ( 58 hom. )

Consequence

TEX26
NM_152325.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.34

Variant links:

Genes affected

TEX26 (HGNC:28622): (testis expressed 26) Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TEX26 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00793907).

BP6

Variant 13-30968931-G-T is Benign according to our data. Variant chr13-30968931-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 710812.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX26	NM_152325.3 linkuse as main transcript	c.693G>T	p.Lys231Asn	missense_variant	6/7	ENST00000380473.8	NP_689538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TEX26	ENST00000380473.8 linkuse as main transcript	c.693G>T	p.Lys231Asn	missense_variant	6/7	1	NM_152325.3	ENSP00000369840	P1
TEX26	ENST00000531960.1 linkuse as main transcript	c.*332G>T		3_prime_UTR_variant, NMD_transcript_variant	5/6	3		ENSP00000435263
TEX26	ENST00000530916.1 linkuse as main transcript	n.73-5915G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00588

AC:

895

AN:

152148

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00169

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00248

Gnomad FIN

AF:

0.00480

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00917

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00611

AC:

1537

AN:

251416

Hom.:

AF XY:

0.00605

AC XY:

822

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.00191

Gnomad AMR exome

AF:

0.00283

Gnomad ASJ exome

AF:

0.0000992

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00281

Gnomad FIN exome

AF:

0.00628

Gnomad NFE exome

AF:

0.0101

Gnomad OTH exome

AF:

0.00587

GnomAD4 exome

AF:

0.00820

AC:

11993

AN:

1461818

Hom.:

Cov.:

AF XY:

0.00791

AC XY:

5754

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.00125

Gnomad4 AMR exome

AF:

0.00275

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00301

Gnomad4 FIN exome

AF:

0.00784

Gnomad4 NFE exome

AF:

0.00969

Gnomad4 OTH exome

AF:

0.00608

GnomAD4 genome

AF:

0.00588

AC:

895

AN:

152266

Hom.:

Cov.:

AF XY:

0.00587

AC XY:

437

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00168

Gnomad4 AMR

AF:

0.00366

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.00480

Gnomad4 NFE

AF:

0.00918

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00764

Hom.:

Bravo

AF:

0.00564

TwinsUK

AF:

0.0102

AC:

ALSPAC

AF:

0.00882

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.00977

AC:

ExAC

AF:

0.00652

AC:

792

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00742

EpiControl

AF:

0.00818

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2023	TEX26: BS2 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.55

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.16

Eigen

Uncertain

0.37

Eigen_PC

Uncertain

0.26

FATHMM_MKL

Benign

0.66

LIST_S2

Benign

0.66

M_CAP

Benign

0.012

MetaRNN

Benign

0.0079

MetaSVM

Uncertain

-0.24

MutationAssessor

Uncertain

2.5

MutationTaster

Benign

0.77

PrimateAI

Uncertain

0.51

PROVEAN

Pathogenic

-4.8

REVEL

Benign

0.25

Sift

Uncertain

0.0030

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.52

MutPred

0.089

Loss of ubiquitination at K231 (P = 0.0027);

MVP

0.27

MPC

0.028

ClinPred

0.028

GERP RS

4.0

Varity_R

0.67

gMVP

0.30

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.17

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