Variant X-105219278-TTGAGTA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2

The NM_031274.5(TEX13A):c.910_915delTACTCA(p.Tyr304_Ser305del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000439 in 1,208,457 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000045 ( 0 hom., 2 hem., cov: 22)

Exomes 𝑓: 0.000044 ( 0 hom. 13 hem. )

Consequence

TEX13A
NM_031274.5 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.59

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]

TEX13A links:

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]

IL1RAPL2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_031274.5.

BP6

Variant X-105219278-TTGAGTA-T is Benign according to our data. Variant chrX-105219278-TTGAGTA-T is described in ClinVar as [Likely_benign]. Clinvar id is 2661119.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX13A	NM_031274.5 linkuse as main transcript	c.910_915delTACTCA	p.Tyr304_Ser305del	conservative_inframe_deletion	3/3	ENST00000600991.6	NP_112564.1	Q9BXU3
IL1RAPL2	NM_017416.2 linkuse as main transcript	c.357-14523_357-14518delTATGAG		intron_variant		ENST00000372582.6	NP_059112.1	Q9NP60
TEX13A	NM_001291277.2 linkuse as main transcript	c.910_915delTACTCA	p.Tyr304_Ser305del	conservative_inframe_deletion	3/3		NP_001278206.1	Q9BXU3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TEX13A	ENST00000600991.6 linkuse as main transcript	c.910_915delTACTCA	p.Tyr304_Ser305del	conservative_inframe_deletion	3/3	1	NM_031274.5	ENSP00000471604.2	Q9BXU3
TEX13A	ENST00000609007.3 linkuse as main transcript	c.910_915delTACTCA	p.Tyr304_Ser305del	conservative_inframe_deletion	3/3	1		ENSP00000477478.2	Q9BXU3
IL1RAPL2	ENST00000372582.6 linkuse as main transcript	c.357-14523_357-14518delTATGAG		intron_variant		1	NM_017416.2	ENSP00000361663.1	Q9NP60

Frequencies

GnomAD3 genomes

AF:

0.0000451

AC:

AN:

110774

Hom.:

Cov.:

AF XY:

0.0000606

AC XY:

AN XY:

33020

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000758

Gnomad EAS

AF:

0.000574

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000189

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000605

AC:

AN:

181697

Hom.:

AF XY:

0.0000593

AC XY:

AN XY:

67503

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000365

Gnomad ASJ exome

AF:

0.000669

Gnomad EAS exome

AF:

0.000221

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000246

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000437

AC:

AN:

1097630

Hom.:

AF XY:

0.0000358

AC XY:

AN XY:

363056

show subpopulations

Gnomad4 AFR exome

AF:

0.0000379

Gnomad4 AMR exome

AF:

0.0000284

Gnomad4 ASJ exome

AF:

0.000877

Gnomad4 EAS exome

AF:

0.0000993

Gnomad4 SAS exome

AF:

0.0000185

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000261

Gnomad4 OTH exome

AF:

0.0000434

GnomAD4 genome

AF:

0.0000451

AC:

AN:

110827

Hom.:

Cov.:

AF XY:

0.0000605

AC XY:

AN XY:

33083

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.000758

Gnomad4 EAS

AF:

0.000576

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000189

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000434

Hom.:

Bravo

AF:

0.0000529

Asia WGS

AF:

0.000398

AC:

AN:

2522

EpiCase

AF:

0.0000545

EpiControl

AF:

0.000119

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

IL1RAPL2: BS2; TEX13A: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over