chrX-118791935-A-G

Position:

• chrX-118791935-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001560.3(IL13RA1):​c.*81A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 506,868 control chromosomes in the GnomAD database, including 8,579 homozygotes. There are 32,199 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.17 (1510 hom., 6144 hem., cov: 23)
  • Exomes 𝑓: 0.21 (7069 hom. 26055 hem.)
• Consequence: IL13RA1 NM_001560.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL13RA1	NM_001560.3	c.*81A>G		3_prime_UTR_variant	11/11	ENST00000371666.8	NP_001551.1
IL13RA1	XM_047442096.1	c.1192-12997A>G		intron_variant			XP_047298052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL13RA1	ENST00000371666.8	c.*81A>G		3_prime_UTR_variant	11/11	1	NM_001560.3	ENSP00000360730.3
IL13RA1	ENST00000652600.1	c.*81A>G		3_prime_UTR_variant	12/12			ENSP00000498980.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 19451 AN: 111661 Hom.: 1511 Cov.: 23 AF XY: 0.181 AC XY: 6127 AN XY: 33857

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.210 AC: 82992 AN: 395152 Hom.: 7069 Cov.: 5 AF XY: 0.225 AC XY: 26055 AN XY: 115878

Gnomad4 AFR exome AF: 0.0962

Gnomad4 AMR exome AF: 0.441

Gnomad4 ASJ exome AF: 0.244

Gnomad4 EAS exome AF: 0.439

Gnomad4 SAS exome AF: 0.286

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.166

Gnomad4 OTH exome AF: 0.205

GnomAD4 genome AF: 0.174 AC: 19465 AN: 111716 Hom.: 1510 Cov.: 23 AF XY: 0.181 AC XY: 6144 AN XY: 33922

Gnomad4 AFR AF: 0.0925

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.212

Alfa AF: 0.171 Hom.: 5901

Bravo AF: 0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	13
DANN	Benign	0.85

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: rs2495636; hg19: chrX-117925898; COSMIC: COSV65424389;