X-70529946-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_031276.3(TEX11):c.2574C>T(p.Thr858=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000753 in 1,209,241 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 40 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.000045 (0 hom., 1 hem., cov: 23)
  • Exomes 𝑓: 0.000078 (0 hom. 39 hem.)
• Consequence: TEX11 NM_031276.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.138

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 Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP6: Variant X-70529946-G-A is Benign according to our data. Variant chrX-70529946-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3025229.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.138 with no splicing effect.
• BS2: High Hemizygotes in GnomAdExome at 17 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX11	NM_031276.3	c.2574C>T	p.Thr858=	synonymous_variant	29/30	ENST00000374333.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX11	ENST00000374333.7	c.2574C>T	p.Thr858=	synonymous_variant	29/30	1	NM_031276.3	P2
TEX11	ENST00000344304.3	c.2619C>T	p.Thr873=	synonymous_variant	28/29	5		A2
TEX11	ENST00000395889.6	c.2619C>T	p.Thr873=	synonymous_variant	30/31	2		A2
TEX11	ENST00000374320.6	c.1644C>T	p.Thr548=	synonymous_variant	18/19	2

Frequencies

GnomAD3 genomes AF: 0.0000447 AC: 5 AN: 111787 Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1 AN XY: 33969

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000381

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00424

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000241 AC: 44 AN: 182693 Hom.: 0 AF XY: 0.000253 AC XY: 17 AN XY: 67191

Gnomad AFR exome AF: 0.0000761

Gnomad AMR exome AF: 0.00128

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: 0.0000857

Gnomad OTH exome AF: 0.000222

GnomAD4 exome AF: 0.0000784 AC: 86 AN: 1097400 Hom.: 0 Cov.: 29 AF XY: 0.000108 AC XY: 39 AN XY: 362786

Gnomad4 AFR exome AF: 0.0000379

Gnomad4 AMR exome AF: 0.00114

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: 0.0000440

Gnomad4 OTH exome AF: 0.0000651

GnomAD4 genome AF: 0.0000447 AC: 5 AN: 111841 Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1 AN XY: 34033

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000381

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000174 Hom.: 1

Bravo AF: 0.000102

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

TEX11: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	1.2
Dann	Benign	0.61

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

Other links and lift over

dbSNP: rs201633202; hg19: chrX-69749796;