Variant X-70554698-A-G 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_031276.3(TEX11):c.2243T>C(p.Val748Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000257 in 1,207,826 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 105 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V748L) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00017 ( 0 hom., 5 hem., cov: 23)

Exomes 𝑓: 0.00027 ( 0 hom. 100 hem. )

Consequence

TEX11
NM_031276.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.46

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 -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.043995053).

BP6

Variant X-70554698-A-G is Benign according to our data. Variant chrX-70554698-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 981147.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Hemizygotes in GnomAd at 5 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX11	NM_031276.3 linkuse as main transcript	c.2243T>C	p.Val748Ala	missense_variant	26/30	ENST00000374333.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX11	ENST00000374333.7 linkuse as main transcript	c.2243T>C	p.Val748Ala	missense_variant	26/30	1	NM_031276.3	P2	Q8IYF3-3
TEX11	ENST00000344304.3 linkuse as main transcript	c.2288T>C	p.Val763Ala	missense_variant	25/29	5		A2	Q8IYF3-1
TEX11	ENST00000395889.6 linkuse as main transcript	c.2288T>C	p.Val763Ala	missense_variant	27/31	2		A2	Q8IYF3-1
TEX11	ENST00000374320.6 linkuse as main transcript	c.1313T>C	p.Val438Ala	missense_variant	15/19	2			Q8IYF3-2

Frequencies

GnomAD3 genomes

AF:

0.000170

AC:

AN:

111847

Hom.:

Cov.:

AF XY:

0.000147

AC XY:

AN XY:

33995

show subpopulations

Gnomad AFR

AF:

0.0000325

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000951

Gnomad ASJ

AF:

0.000756

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000329

Gnomad MID

AF:

0.00837

Gnomad NFE

AF:

0.000169

Gnomad OTH

AF:

0.00133

GnomAD3 exomes

AF:

0.000257

AC:

AN:

178986

Hom.:

AF XY:

0.000173

AC XY:

AN XY:

63722

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000189

Gnomad ASJ exome

AF:

0.00217

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000166

Gnomad FIN exome

AF:

0.000125

Gnomad NFE exome

AF:

0.000211

Gnomad OTH exome

AF:

0.000683

GnomAD4 exome

AF:

0.000266

AC:

291

AN:

1095926

Hom.:

Cov.:

AF XY:

0.000277

AC XY:

100

AN XY:

361568

show subpopulations

Gnomad4 AFR exome

AF:

0.000190

Gnomad4 AMR exome

AF:

0.000200

Gnomad4 ASJ exome

AF:

0.00155

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000447

Gnomad4 FIN exome

AF:

0.000272

Gnomad4 NFE exome

AF:

0.000209

Gnomad4 OTH exome

AF:

0.000522

GnomAD4 genome

AF:

0.000170

AC:

AN:

111900

Hom.:

Cov.:

AF XY:

0.000147

AC XY:

AN XY:

34058

show subpopulations

Gnomad4 AFR

AF:

0.0000324

Gnomad4 AMR

AF:

0.0000950

Gnomad4 ASJ

AF:

0.000756

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000329

Gnomad4 NFE

AF:

0.000170

Gnomad4 OTH

AF:

0.00131

Alfa

AF:

0.000320

Hom.:

Bravo

AF:

0.000253

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ExAC

AF:

0.000198

AC:

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Aug 05, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.52

Cadd

Benign

Dann

Uncertain

0.99

FATHMM_MKL

Uncertain

0.79

LIST_S2

Benign

0.43

T;T;T;.

M_CAP

Benign

0.0065

MetaRNN

Benign

0.044

T;T;T;T

MetaSVM

Benign

-0.99

MutationTaster

Benign

0.94

N;N;N;N

PrimateAI

Benign

0.40

PROVEAN

Benign

-2.3

N;D;N;N

REVEL

Benign

0.11

Sift

Uncertain

0.013

D;D;D;D

Sift4G

Uncertain

0.013

D;D;D;D

Polyphen

0.0080

B;.;B;B

Vest4

0.60

MVP

0.30

MPC

0.93

ClinPred

0.071

GERP RS

2.0

Varity_R

0.14

gMVP

0.29

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