X-105219278-TTGAGTA-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4 BP6_Moderate BS2

The NM_031274.5(TEX13A):c.910_915del(p.Tyr304_Ser305del) variant causes a 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 inframe_deletion
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.59

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]

ACMG classification

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 GnomAd at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX13A	NM_031274.5	c.910_915del	p.Tyr304_Ser305del	inframe_deletion	3/3	ENST00000600991.6
IL1RAPL2	NM_017416.2	c.357-14523_357-14518del		intron_variant		ENST00000372582.6
TEX13A	NM_001291277.2	c.910_915del	p.Tyr304_Ser305del	inframe_deletion	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX13A	ENST00000600991.6	c.910_915del	p.Tyr304_Ser305del	inframe_deletion	3/3	1	NM_031274.5	P1
TEX13A	ENST00000609007.3	c.910_915del	p.Tyr304_Ser305del	inframe_deletion	3/3	1		P1
IL1RAPL2	ENST00000372582.6	c.357-14523_357-14518del		intron_variant		1	NM_017416.2	P1

Frequencies

GnomAD3 genomes AF: 0.0000451 AC: 5 AN: 110774 Hom.: 0 Cov.: 22 AF XY: 0.0000606 AC XY: 2 AN XY: 33020

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: 11 AN: 181697 Hom.: 0 AF XY: 0.0000593 AC XY: 4 AN XY: 67503

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: 48 AN: 1097630 Hom.: 0 AF XY: 0.0000358 AC XY: 13 AN XY: 363056

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: 5 AN: 110827 Hom.: 0 Cov.: 22 AF XY: 0.0000605 AC XY: 2 AN XY: 33083

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.: 0

Bravo AF: 0.0000529

Asia WGS AF: 0.000398 AC: 1 AN: 2522

EpiCase AF: 0.0000545

EpiControl AF: 0.000119

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

Nov 01, 2022

IL1RAPL2: BS2; TEX13A: BS2 -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs782595598; hg19: chrX-104463960;