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GeneBe

X-70552201-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_031276.3(TEX11):c.2445G>A(p.Ala815=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,209,230 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 59 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 0.000080 ( 0 hom., 4 hem., cov: 23)
Exomes 𝑓: 0.00012 ( 0 hom. 55 hem. )

Consequence

TEX11
NM_031276.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.76
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 -11 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=-0.75).
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-70552201-C-T is Benign according to our data. Variant chrX-70552201-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3047254.Status of the report is criteria_provided_single_submitter, 1 stars.
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=-1.76 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Hemizygotes in GnomAd at 4 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TEX11NM_031276.3 linkuse as main transcriptc.2445G>A p.Ala815= synonymous_variant 28/30 ENST00000374333.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TEX11ENST00000374333.7 linkuse as main transcriptc.2445G>A p.Ala815= synonymous_variant 28/301 NM_031276.3 P2Q8IYF3-3
TEX11ENST00000344304.3 linkuse as main transcriptc.2490G>A p.Ala830= synonymous_variant 27/295 A2Q8IYF3-1
TEX11ENST00000395889.6 linkuse as main transcriptc.2490G>A p.Ala830= synonymous_variant 29/312 A2Q8IYF3-1
TEX11ENST00000374320.6 linkuse as main transcriptc.1515G>A p.Ala505= synonymous_variant 17/192 Q8IYF3-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0000805
AC:
9
AN:
111862
Hom.:
0
Cov.:
23
AF XY:
0.000118
AC XY:
4
AN XY:
34034
show subpopulations
Gnomad AFR
AF:
0.0000973
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.000113
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000115
AC:
21
AN:
182269
Hom.:
0
AF XY:
0.000180
AC XY:
12
AN XY:
66761
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000735
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000364
Gnomad SAS exome
AF:
0.000425
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000737
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000123
AC:
135
AN:
1097368
Hom.:
0
Cov.:
29
AF XY:
0.000152
AC XY:
55
AN XY:
362782
show subpopulations
Gnomad4 AFR exome
AF:
0.0000379
Gnomad4 AMR exome
AF:
0.0000569
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000166
Gnomad4 SAS exome
AF:
0.000500
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000108
Gnomad4 OTH exome
AF:
0.000174
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0000805
AC:
9
AN:
111862
Hom.:
0
Cov.:
23
AF XY:
0.000118
AC XY:
4
AN XY:
34034
show subpopulations
Gnomad4 AFR
AF:
0.0000973
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000113
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000214
Hom.:
1
Bravo
AF:
0.0000793
EpiCase
AF:
0.000110
EpiControl
AF:
0.000120

ClinVar

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

Submissions by phenotype

TEX11-related disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesApr 01, 2019This variant is classified as likely 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
-0.75
Cadd
Benign
0.27
Dann
Benign
0.34

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: rs376114732; hg19: chrX-69772051; API