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GeneBe

X-105220239-T-G

Variant summary

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

The NM_031274.5(TEX13A):c.159A>C(p.Ile53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 1,210,085 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 73 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 0.00012 ( 0 hom., 3 hem., cov: 23)
Exomes 𝑓: 0.00018 ( 0 hom. 70 hem. )

Consequence

TEX13A
NM_031274.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.759
Variant links:
Genes affected
TEX13A (HGNC:11735): (testis expressed 13A) This gene is similar to a mouse gene that is expressed in the testis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
IL1RAPL2 (HGNC:5997): (interleukin 1 receptor accessory protein like 2) The protein encoded by this gene is a member of the interleukin 1 receptor family. This protein is similar to the interleukin 1 accessory proteins, and is most closely related to interleukin 1 receptor accessory protein-like 1 (IL1RAPL1). This gene and IL1RAPL1 are located at a region on chromosome X that is associated with X-linked non-syndromic cognitive disability. [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=-0.83).
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-105220239-T-G is Benign according to our data. Variant chrX-105220239-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2661122.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=0.759 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 3 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TEX13ANM_031274.5 linkuse as main transcriptc.159A>C p.Ile53= synonymous_variant 2/3 ENST00000600991.6
IL1RAPL2NM_017416.2 linkuse as main transcriptc.357-13579T>G intron_variant ENST00000372582.6
TEX13ANM_001291277.2 linkuse as main transcriptc.159A>C p.Ile53= synonymous_variant 2/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TEX13AENST00000600991.6 linkuse as main transcriptc.159A>C p.Ile53= synonymous_variant 2/31 NM_031274.5 P1
TEX13AENST00000609007.3 linkuse as main transcriptc.159A>C p.Ile53= synonymous_variant 2/31 P1
IL1RAPL2ENST00000372582.6 linkuse as main transcriptc.357-13579T>G intron_variant 1 NM_017416.2 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000116
AC:
13
AN:
112027
Hom.:
0
Cov.:
23
AF XY:
0.0000877
AC XY:
3
AN XY:
34195
show subpopulations
Gnomad AFR
AF:
0.0000324
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000188
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:
0.000188
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000153
AC:
28
AN:
183015
Hom.:
0
AF XY:
0.0000444
AC XY:
3
AN XY:
67513
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000730
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000633
Gnomad NFE exome
AF:
0.000293
Gnomad OTH exome
AF:
0.000222
GnomAD4 exome
AF:
0.000179
AC:
196
AN:
1098006
Hom.:
0
Cov.:
32
AF XY:
0.000193
AC XY:
70
AN XY:
363416
show subpopulations
Gnomad4 AFR exome
AF:
0.0000379
Gnomad4 AMR exome
AF:
0.0000568
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000331
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000495
Gnomad4 NFE exome
AF:
0.000216
Gnomad4 OTH exome
AF:
0.000174
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000116
AC:
13
AN:
112079
Hom.:
0
Cov.:
23
AF XY:
0.0000876
AC XY:
3
AN XY:
34257
show subpopulations
Gnomad4 AFR
AF:
0.0000323
Gnomad4 AMR
AF:
0.000188
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000188
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000106
EpiCase
AF:
0.0000545
EpiControl
AF:
0.0000593

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2023TEX13A: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
3.9
Dann
Benign
0.75

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs782379343; hg19: chrX-104464923; API