X-118786645-A-G

Variant names:

• chrX-118786645-A-G
• rs2495632
• NM_001560.3:c.1192-5117A>G

Variant summary

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

The NM_001560.3(IL13RA1):​c.1192-5117A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 111,022 control chromosomes in the GnomAD database, including 4,313 homozygotes. There are 9,757 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 0.29 (4313 hom., 9757 hem., cov: 23)
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13RA1	NM_001560.3	c.1192-5117A>G		intron_variant	Intron 10 of 10	ENST00000371666.8	NP_001551.1
IL13RA1	XM_047442096.1	c.1191+10134A>G		intron_variant	Intron 10 of 10		XP_047298052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL13RA1	ENST00000371666.8	c.1192-5117A>G		intron_variant	Intron 10 of 10	1	NM_001560.3	ENSP00000360730.3
IL13RA1	ENST00000652600.1	c.1186-5117A>G		intron_variant	Intron 11 of 11			ENSP00000498980.1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 32420 AN: 110969 Hom.: 4313 Cov.: 23

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.0452

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.292 AC: 32442 AN: 111022 Hom.: 4313 Cov.: 23 AF XY: 0.293 AC XY: 9757 AN XY: 33308

African (AFR) AF: 0.483 AC: 14705 AN: 30436

American (AMR) AF: 0.417 AC: 4344 AN: 10427

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 664 AN: 2638

East Asian (EAS) AF: 0.447 AC: 1565 AN: 3499

South Asian (SAS) AF: 0.318 AC: 855 AN: 2685

European-Finnish (FIN) AF: 0.195 AC: 1159 AN: 5940

Middle Eastern (MID) AF: 0.356 AC: 77 AN: 216

European-Non Finnish (NFE) AF: 0.162 AC: 8564 AN: 52981

Other (OTH) AF: 0.316 AC: 478 AN: 1514

Alfa AF: 0.241 Hom.: 1469

Bravo AF: 0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.35
PhyloP100		-2.0
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: rs2495632; hg19: chrX-117920608;