X-118770125-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001560.3(IL13RA1):c.1009+3149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00155 in 266,902 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 114 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 0.0014 (0 hom., 44 hem., cov: 24)
  • Exomes 𝑓: 0.0017 (0 hom. 70 hem.)
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.568

Genes affected

IL13RA1 (HGNC:5974): (interleukin 13 receptor subunit alpha 1) The protein encoded by this gene is a subunit of the interleukin 13 receptor. This subunit forms a receptor complex with IL4 receptor alpha, a subunit shared by IL13 and IL4 receptors. This subunit serves as a primary IL13-binding subunit of the IL13 receptor, and may also be a component of IL4 receptors. This protein has been shown to bind tyrosine kinase TYK2, and thus may mediate the signaling processes that lead to the activation of JAK1, STAT3 and STAT6 induced by IL13 and IL4. [provided by RefSeq, Jul 2008]

TMEM30BP1 (HGNC:55058): (TMEM30B pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BP6: Variant X-118770125-C-T is Benign according to our data. Variant chrX-118770125-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2661274.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAd at 44 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL13RA1	NM_001560.3	c.1009+3149C>T		intron_variant		ENST00000371666.8
IL13RA1	XM_047442096.1	c.1009+3149C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL13RA1	ENST00000371666.8	c.1009+3149C>T		intron_variant		1	NM_001560.3	P1
TMEM30BP1	ENST00000506969.1	n.330C>T		non_coding_transcript_exon_variant	1/1
IL13RA1	ENST00000652600.1	c.1003+3149C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00138 AC: 155 AN: 112185 Hom.: 0 Cov.: 24 AF XY: 0.00128 AC XY: 44 AN XY: 34351

Gnomad AFR AF: 0.000389

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00141

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000734

Gnomad FIN AF: 0.000163

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00233

Gnomad OTH AF: 0.000662

GnomAD4 exome AF: 0.00168 AC: 260 AN: 154665 Hom.: 0 Cov.: 0 AF XY: 0.00124 AC XY: 70 AN XY: 56377

Gnomad4 AFR exome AF: 0.000672

Gnomad4 AMR exome AF: 0.000712

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000340

Gnomad4 FIN exome AF: 0.000274

Gnomad4 NFE exome AF: 0.00258

Gnomad4 OTH exome AF: 0.00167

GnomAD4 genome AF: 0.00138 AC: 155 AN: 112237 Hom.: 0 Cov.: 24 AF XY: 0.00128 AC XY: 44 AN XY: 34413

Gnomad4 AFR AF: 0.000388

Gnomad4 AMR AF: 0.00140

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000736

Gnomad4 FIN AF: 0.000163

Gnomad4 NFE AF: 0.00233

Gnomad4 OTH AF: 0.000654

Alfa AF: 0.00194 Hom.: 11

Bravo AF: 0.00122

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

IL13RA1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	3.8
Dann	Benign	0.89

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

Other links and lift over

dbSNP: rs771636060; hg19: chrX-117904088;