Variant X-70552150-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_031276.3(TEX11):c.2496T>C(p.Asp832=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0624 in 1,209,064 control chromosomes in the GnomAD database, including 3,399 homozygotes. There are 25,679 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.080 ( 426 hom., 2749 hem., cov: 22)

Exomes 𝑓: 0.061 ( 2973 hom. 22930 hem. )

Consequence

TEX11
NM_031276.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.52

Variant links:

Genes affected

TEX11 (HGNC:11733): (testis expressed 11) This gene is X-linked and is expressed in only male germ cells. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

TEX11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant X-70552150-A-G is Benign according to our data. Variant chrX-70552150-A-G is described in ClinVar as [Benign]. Clinvar id is 3059578.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-70552150-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.52 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX11	NM_031276.3 linkuse as main transcript	c.2496T>C	p.Asp832=	synonymous_variant	28/30	ENST00000374333.7	NP_112566.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX11	ENST00000374333.7 linkuse as main transcript	c.2496T>C	p.Asp832=	synonymous_variant	28/30	1	NM_031276.3	ENSP00000363453	P2	Q8IYF3-3
TEX11	ENST00000344304.3 linkuse as main transcript	c.2541T>C	p.Asp847=	synonymous_variant	27/29	5		ENSP00000340995	A2	Q8IYF3-1
TEX11	ENST00000395889.6 linkuse as main transcript	c.2541T>C	p.Asp847=	synonymous_variant	29/31	2		ENSP00000379226	A2	Q8IYF3-1
TEX11	ENST00000374320.6 linkuse as main transcript	c.1566T>C	p.Asp522=	synonymous_variant	17/19	2		ENSP00000363440		Q8IYF3-2

Frequencies

GnomAD3 genomes

AF:

0.0798

AC:

8919

AN:

111827

Hom.:

421

Cov.:

AF XY:

0.0806

AC XY:

2741

AN XY:

34017

show subpopulations

Gnomad AFR

AF:

0.0944

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.246

Gnomad ASJ

AF:

0.0459

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.0193

Gnomad MID

AF:

0.0583

Gnomad NFE

AF:

0.0404

Gnomad OTH

AF:

0.0878

GnomAD3 exomes

AF:

0.112

AC:

20199

AN:

181021

Hom.:

1758

AF XY:

0.0999

AC XY:

6555

AN XY:

65593

show subpopulations

Gnomad AFR exome

AF:

0.0974

Gnomad AMR exome

AF:

0.361

Gnomad ASJ exome

AF:

0.0460

Gnomad EAS exome

AF:

0.136

Gnomad SAS exome

AF:

0.175

Gnomad FIN exome

AF:

0.0256

Gnomad NFE exome

AF:

0.0374

Gnomad OTH exome

AF:

0.0845

GnomAD4 exome

AF:

0.0606

AC:

66496

AN:

1097183

Hom.:

2973

Cov.:

AF XY:

0.0632

AC XY:

22930

AN XY:

362653

show subpopulations

Gnomad4 AFR exome

AF:

0.100

Gnomad4 AMR exome

AF:

0.353

Gnomad4 ASJ exome

AF:

0.0507

Gnomad4 EAS exome

AF:

0.125

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.0289

Gnomad4 NFE exome

AF:

0.0393

Gnomad4 OTH exome

AF:

0.0613

GnomAD4 genome

AF:

0.0799

AC:

8935

AN:

111881

Hom.:

426

Cov.:

AF XY:

0.0807

AC XY:

2749

AN XY:

34081

show subpopulations

Gnomad4 AFR

AF:

0.0944

Gnomad4 AMR

AF:

0.247

Gnomad4 ASJ

AF:

0.0459

Gnomad4 EAS

AF:

0.122

Gnomad4 SAS

AF:

0.174

Gnomad4 FIN

AF:

0.0193

Gnomad4 NFE

AF:

0.0404

Gnomad4 OTH

AF:

0.0866

Alfa

AF:

0.0467

Hom.:

1289

Bravo

AF:

0.101

EpiCase

AF:

0.0373

EpiControl

AF:

0.0338

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TEX11-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 27, 2019

This variant is classified as 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

BayesDel_noAF

Benign

-0.56

CADD

Benign

4.1

DANN

Benign

0.47

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