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

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_031276.3(TEX11):c.2496T>G(p.Asp832Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000633 in 1,209,155 control chromosomes in the GnomAD database, including 8 homozygotes. There are 238 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00039 ( 0 hom., 13 hem., cov: 22)

Exomes 𝑓: 0.00066 ( 8 hom. 225 hem. )

Consequence

TEX11
NM_031276.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter 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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0055111945).

BP6

Variant X-70552150-A-C is Benign according to our data. Variant chrX-70552150-A-C is described in ClinVar as [Benign]. Clinvar id is 789463.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000657 (721/1097254) while in subpopulation EAS AF= 0.022 (664/30173). AF 95% confidence interval is 0.0206. There are 8 homozygotes in gnomad4_exome. There are 225 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 13 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX11	NM_031276.3 linkuse as main transcript	c.2496T>G	p.Asp832Glu	missense_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>G	p.Asp832Glu	missense_variant	28/30	1	NM_031276.3	ENSP00000363453	P2	Q8IYF3-3
TEX11	ENST00000344304.3 linkuse as main transcript	c.2541T>G	p.Asp847Glu	missense_variant	27/29	5		ENSP00000340995	A2	Q8IYF3-1
TEX11	ENST00000395889.6 linkuse as main transcript	c.2541T>G	p.Asp847Glu	missense_variant	29/31	2		ENSP00000379226	A2	Q8IYF3-1
TEX11	ENST00000374320.6 linkuse as main transcript	c.1566T>G	p.Asp522Glu	missense_variant	17/19	2		ENSP00000363440		Q8IYF3-2

Frequencies

GnomAD3 genomes

AF:

0.000393

AC:

AN:

111847

Hom.:

Cov.:

AF XY:

0.000382

AC XY:

AN XY:

34027

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000192

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0112

Gnomad SAS

AF:

0.000377

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000188

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000956

AC:

173

AN:

181021

Hom.:

AF XY:

0.000869

AC XY:

AN XY:

65593

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000745

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0105

Gnomad SAS exome

AF:

0.000489

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000123

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000657

AC:

721

AN:

1097254

Hom.:

Cov.:

AF XY:

0.000620

AC XY:

225

AN XY:

362674

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000600

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0220

Gnomad4 SAS exome

AF:

0.000315

Gnomad4 FIN exome

AF:

0.0000247

Gnomad4 NFE exome

AF:

0.00000832

Gnomad4 OTH exome

AF:

0.000239

GnomAD4 genome

AF:

0.000393

AC:

AN:

111901

Hom.:

Cov.:

AF XY:

0.000381

AC XY:

AN XY:

34091

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000192

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0112

Gnomad4 SAS

AF:

0.000378

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000188

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000113

Hom.:

1289

ExAC

AF:

0.000914

AC:

111

EpiCase

AF:

0.00

EpiControl

AF:

0.0000597

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.19

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Benign

0.50

DEOGEN2

Benign

0.034

.;.;T;T

FATHMM_MKL

Benign

0.59

LIST_S2

Benign

0.71

T;T;T;.

MetaRNN

Benign

0.0055

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.97

.;.;L;L

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.40

N;N;N;N

REVEL

Benign

0.022

Sift

Benign

0.83

T;T;T;T

Sift4G

Benign

0.85

T;T;T;T

Polyphen

0.88

P;.;P;P

Vest4

0.053

MutPred

0.29

.;.;Gain of solvent accessibility (P = 0.1751);Gain of solvent accessibility (P = 0.1751);

MVP

0.41

MPC

0.59

ClinPred

0.065

GERP RS

2.5

Varity_R

0.066

gMVP

0.070

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