X-118729785-A-G

Variant names:

• chrX-118729785-A-G
• rs2250747
• NM_001560.3:c.88+2059A>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.88+2059A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 111,652 control chromosomes in the GnomAD database, including 1,489 homozygotes. There are 6,052 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 (1489 hom., 6052 hem., cov: 23)
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13RA1	NM_001560.3	MANE Select	c.88+2059A>G		intron	N/A	NP_001551.1	P78552-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13RA1	ENST00000371666.8	TSL:1 MANE Select	c.88+2059A>G		intron	N/A	ENSP00000360730.3	P78552-1
	IL13RA1	ENST00000371642.1	TSL:1	c.88+2059A>G		intron	N/A	ENSP00000360705.1	P78552-2
	IL13RA1	ENST00000965042.1		c.88+2059A>G		intron	N/A	ENSP00000635101.1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 19106 AN: 111600 Hom.: 1490 Cov.: 23

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.0453

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.171 AC: 19108 AN: 111652 Hom.: 1489 Cov.: 23 AF XY: 0.179 AC XY: 6052 AN XY: 33830

African (AFR) AF: 0.0716 AC: 2206 AN: 30798

American (AMR) AF: 0.352 AC: 3693 AN: 10488

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 659 AN: 2649

East Asian (EAS) AF: 0.407 AC: 1425 AN: 3505

South Asian (SAS) AF: 0.309 AC: 841 AN: 2724

European-Finnish (FIN) AF: 0.196 AC: 1166 AN: 5958

Middle Eastern (MID) AF: 0.298 AC: 64 AN: 215

European-Non Finnish (NFE) AF: 0.164 AC: 8698 AN: 53111

Other (OTH) AF: 0.214 AC: 325 AN: 1519

Alfa AF: 0.173 Hom.: 3090

Bravo AF: 0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.14
DANN	Benign	0.67
PhyloP100		-0.75
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: rs2250747; hg19: chrX-117863748;