rs1892299

Variant names:

• chrX-118743474-G-A
• rs1892299
• NM_001560.3:c.228+2318G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001560.3(IL13RA1):​c.228+2318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 110,300 control chromosomes in the GnomAD database, including 3,584 homozygotes. There are 8,859 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 0.27 (3584 hom., 8859 hem., cov: 22)
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001560.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13RA1	NM_001560.3	MANE Select	c.228+2318G>A		intron	N/A	NP_001551.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13RA1	ENST00000371666.8	TSL:1 MANE Select	c.228+2318G>A		intron	N/A	ENSP00000360730.3
	IL13RA1	ENST00000371642.1	TSL:1	c.228+2318G>A		intron	N/A	ENSP00000360705.1
	IL13RA1	ENST00000652600.1		c.222+2318G>A		intron	N/A	ENSP00000498980.1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 30065 AN: 110243 Hom.: 3583 Cov.: 22

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.0427

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.291

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.273 AC: 30083 AN: 110300 Hom.: 3584 Cov.: 22 AF XY: 0.272 AC XY: 8859 AN XY: 32578

African (AFR) AF: 0.417 AC: 12612 AN: 30247

American (AMR) AF: 0.406 AC: 4176 AN: 10280

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 651 AN: 2623

East Asian (EAS) AF: 0.409 AC: 1426 AN: 3483

South Asian (SAS) AF: 0.307 AC: 803 AN: 2616

European-Finnish (FIN) AF: 0.196 AC: 1133 AN: 5793

Middle Eastern (MID) AF: 0.330 AC: 70 AN: 212

European-Non Finnish (NFE) AF: 0.165 AC: 8740 AN: 52853

Other (OTH) AF: 0.293 AC: 443 AN: 1514

Alfa AF: 0.261 Hom.: 1891

Bravo AF: 0.303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.18
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1892299; hg19: chrX-117877437;