X-70529893-C-A

Position:

• chrX-70529893-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_031276.3(TEX11):​c.2627G>T​(p.Gly876Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 22)
• Consequence: TEX11 NM_031276.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.309

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3282882).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX11	NM_031276.3	c.2627G>T	p.Gly876Val	missense_variant	29/30	ENST00000374333.7	NP_112566.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX11	ENST00000374333.7	c.2627G>T	p.Gly876Val	missense_variant	29/30	1	NM_031276.3	ENSP00000363453.2
TEX11	ENST00000344304.3	c.2672G>T	p.Gly891Val	missense_variant	28/29	5		ENSP00000340995.3
TEX11	ENST00000395889.6	c.2672G>T	p.Gly891Val	missense_variant	30/31	2		ENSP00000379226.2
TEX11	ENST00000374320.6	c.1697G>T	p.Gly566Val	missense_variant	18/19	2		ENSP00000363440.2

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 22

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 10, 2024

The c.2672G>T (p.G891V) alteration is located in exon 30 (coding exon 28) of the TEX11 gene. This alteration results from a G to T substitution at nucleotide position 2672, causing the glycine (G) at amino acid position 891 to be replaced by a valine (V). 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	0.22
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.8
DANN	Uncertain	0.98
DEOGEN2	Uncertain	0.48	.;.;T;T
FATHMM_MKL	Benign	0.085	N
LIST_S2	Benign	0.82	T;T;T;.
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.33	T;T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Uncertain	2.2	.;.;M;M
PrimateAI	Benign	0.19	T
PROVEAN	Uncertain	-3.7	D;D;D;D
REVEL	Benign	0.14
Sift	Uncertain	0.024	D;D;D;D
Sift4G	Benign	0.072	T;T;T;T
Polyphen		0.96	D;.;P;P
Vest4		0.42
MutPred		0.40		.;.;Gain of MoRF binding (P = 0.1198);Gain of MoRF binding (P = 0.1198);
MVP		0.22
MPC		0.60
ClinPred		0.83	D
GERP RS		-3.6
Varity_R		0.17
gMVP		0.49

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-69749743;