Variant X-70554791-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_031276.3(TEX11):c.2150C>T(p.Ser717Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000999 in 1,200,983 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000027 ( 0 hom., 1 hem., cov: 23)

Exomes 𝑓: 0.0000083 ( 0 hom. 4 hem. )

Consequence

TEX11
NM_031276.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.94

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 Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.18039906).

BS2

High Hemizygotes in GnomAdExome4 at 4 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX11	NM_031276.3 linkuse as main transcript	c.2150C>T	p.Ser717Leu	missense_variant	26/30	ENST00000374333.7	NP_112566.2	Q8IYF3-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TEX11	ENST00000374333.7 linkuse as main transcript	c.2150C>T	p.Ser717Leu	missense_variant	26/30	1	NM_031276.3	ENSP00000363453.2	Q8IYF3-3
TEX11	ENST00000344304.3 linkuse as main transcript	c.2195C>T	p.Ser732Leu	missense_variant	25/29	5		ENSP00000340995.3	Q8IYF3-1
TEX11	ENST00000395889.6 linkuse as main transcript	c.2195C>T	p.Ser732Leu	missense_variant	27/31	2		ENSP00000379226.2	Q8IYF3-1
TEX11	ENST00000374320.6 linkuse as main transcript	c.1220C>T	p.Ser407Leu	missense_variant	15/19	2		ENSP00000363440.2	Q8IYF3-2

Frequencies

GnomAD3 genomes

AF:

0.0000269

AC:

AN:

111696

Hom.:

Cov.:

AF XY:

0.0000295

AC XY:

AN XY:

33880

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000955

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000377

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000583

AC:

AN:

171487

Hom.:

AF XY:

0.00

AC XY:

AN XY:

57271

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000128

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000826

AC:

AN:

1089287

Hom.:

Cov.:

AF XY:

0.0000112

AC XY:

AN XY:

355719

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000107

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000269

AC:

AN:

111696

Hom.:

Cov.:

AF XY:

0.0000295

AC XY:

AN XY:

33880

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.0000955

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000377

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000151

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000149

AC:

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Inborn genetic diseases

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 29, 2024

The c.2195C>T (p.S732L) alteration is located in exon 27 (coding exon 25) of the TEX11 gene. This alteration results from a C to T substitution at nucleotide position 2195, causing the serine (S) at amino acid position 732 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.19

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.16

.;.;T;T

FATHMM_MKL

Benign

0.75

LIST_S2

Benign

0.83

T;T;T;.

M_CAP

Benign

0.016

MetaRNN

Benign

0.18

T;T;T;T

MetaSVM

Benign

-0.84

MutationAssessor

Uncertain

2.2

.;.;M;M

PrimateAI

Benign

0.40

PROVEAN

Uncertain

-3.0

D;D;D;D

REVEL

Benign

0.14

Sift

Benign

0.034

D;D;D;D

Sift4G

Benign

0.070

T;T;T;T

Polyphen

1.0

D;.;D;D

Vest4

0.11

MVP

0.23

MPC

0.29

ClinPred

0.83

GERP RS

4.5

Varity_R

0.16

gMVP

0.24

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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