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GeneBe

X-70552150-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_031276.3(TEX11):c.2496T>C(p.Asp832=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0624 in 1,209,064 control chromosomes in the GnomAD database, including 3,399 homozygotes. There are 25,679 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.080 ( 426 hom., 2749 hem., cov: 22)
Exomes 𝑓: 0.061 ( 2973 hom. 22930 hem. )

Consequence

TEX11
NM_031276.3 synonymous

Scores

2

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-70552150-A-G is Benign according to our data. Variant chrX-70552150-A-G is described in ClinVar as [Benign]. Clinvar id is 3059578.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-70552150-A-G is described in Lovd as [Benign].
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.52 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TEX11NM_031276.3 linkuse as main transcriptc.2496T>C p.Asp832= synonymous_variant 28/30 ENST00000374333.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TEX11ENST00000374333.7 linkuse as main transcriptc.2496T>C p.Asp832= synonymous_variant 28/301 NM_031276.3 P2Q8IYF3-3
TEX11ENST00000344304.3 linkuse as main transcriptc.2541T>C p.Asp847= synonymous_variant 27/295 A2Q8IYF3-1
TEX11ENST00000395889.6 linkuse as main transcriptc.2541T>C p.Asp847= synonymous_variant 29/312 A2Q8IYF3-1
TEX11ENST00000374320.6 linkuse as main transcriptc.1566T>C p.Asp522= synonymous_variant 17/192 Q8IYF3-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0798
AC:
8919
AN:
111827
Hom.:
421
Cov.:
22
AF XY:
0.0806
AC XY:
2741
AN XY:
34017
show subpopulations
Gnomad AFR
AF:
0.0944
Gnomad AMI
AF:
0.0307
Gnomad AMR
AF:
0.246
Gnomad ASJ
AF:
0.0459
Gnomad EAS
AF:
0.123
Gnomad SAS
AF:
0.172
Gnomad FIN
AF:
0.0193
Gnomad MID
AF:
0.0583
Gnomad NFE
AF:
0.0404
Gnomad OTH
AF:
0.0878
GnomAD3 exomes
AF:
0.112
AC:
20199
AN:
181021
Hom.:
1758
AF XY:
0.0999
AC XY:
6555
AN XY:
65593
show subpopulations
Gnomad AFR exome
AF:
0.0974
Gnomad AMR exome
AF:
0.361
Gnomad ASJ exome
AF:
0.0460
Gnomad EAS exome
AF:
0.136
Gnomad SAS exome
AF:
0.175
Gnomad FIN exome
AF:
0.0256
Gnomad NFE exome
AF:
0.0374
Gnomad OTH exome
AF:
0.0845
GnomAD4 exome
AF:
0.0606
AC:
66496
AN:
1097183
Hom.:
2973
Cov.:
30
AF XY:
0.0632
AC XY:
22930
AN XY:
362653
show subpopulations
Gnomad4 AFR exome
AF:
0.100
Gnomad4 AMR exome
AF:
0.353
Gnomad4 ASJ exome
AF:
0.0507
Gnomad4 EAS exome
AF:
0.125
Gnomad4 SAS exome
AF:
0.176
Gnomad4 FIN exome
AF:
0.0289
Gnomad4 NFE exome
AF:
0.0393
Gnomad4 OTH exome
AF:
0.0613
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0799
AC:
8935
AN:
111881
Hom.:
426
Cov.:
22
AF XY:
0.0807
AC XY:
2749
AN XY:
34081
show subpopulations
Gnomad4 AFR
AF:
0.0944
Gnomad4 AMR
AF:
0.247
Gnomad4 ASJ
AF:
0.0459
Gnomad4 EAS
AF:
0.122
Gnomad4 SAS
AF:
0.174
Gnomad4 FIN
AF:
0.0193
Gnomad4 NFE
AF:
0.0404
Gnomad4 OTH
AF:
0.0866
Alfa
AF:
0.0467
Hom.:
1289
Bravo
AF:
0.101
EpiCase
AF:
0.0373
EpiControl
AF:
0.0338

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

TEX11-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesMar 27, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
4.1
Dann
Benign
0.47

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.

Other links and lift over

dbSNP: rs16991177; hg19: chrX-69772000; COSMIC: COSV60231179; API