rs5946040

Variant names:

• chrX-115013203-T-G
• rs5946040
• NM_000640.3:c.521+566A>C

Variant summary

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

The NM_000640.3(IL13RA2):​c.521+566A>C 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 110,328 control chromosomes in the GnomAD database, including 4,975 homozygotes. There are 8,134 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 (4975 hom., 8134 hem., cov: 22)
• Consequence: IL13RA2 NM_000640.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 3 publications found

Genes affected

IL13RA2 (HGNC:5975): (interleukin 13 receptor subunit alpha 2) The protein encoded by this gene is closely related to Il13RA1, a subuint of the interleukin 13 receptor complex. This protein binds IL13 with high affinity, but lacks cytoplasmic domain, and does not appear to function as a signal mediator. It is reported to play a role in the internalization of IL13. [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 = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13RA2	NM_000640.3	c.521+566A>C		intron_variant	Intron 5 of 9	ENST00000243213.2	NP_000631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL13RA2	ENST00000243213.2	c.521+566A>C		intron_variant	Intron 5 of 9	1	NM_000640.3	ENSP00000243213.1
IL13RA2	ENST00000371936.5	c.521+566A>C		intron_variant	Intron 6 of 10	5		ENSP00000361004.1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 30073 AN: 110273 Hom.: 4969 Cov.: 22

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00541

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0983

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.273 AC: 30121 AN: 110328 Hom.: 4975 Cov.: 22 AF XY: 0.249 AC XY: 8134 AN XY: 32602

African (AFR) AF: 0.622 AC: 18688 AN: 30021

American (AMR) AF: 0.135 AC: 1401 AN: 10378

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 464 AN: 2642

East Asian (EAS) AF: 0.00543 AC: 19 AN: 3500

South Asian (SAS) AF: 0.119 AC: 310 AN: 2596

European-Finnish (FIN) AF: 0.0983 AC: 582 AN: 5920

Middle Eastern (MID) AF: 0.200 AC: 43 AN: 215

European-Non Finnish (NFE) AF: 0.155 AC: 8173 AN: 52861

Other (OTH) AF: 0.200 AC: 302 AN: 1510

Alfa AF: 0.230 Hom.: 1882

Bravo AF: 0.293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	8.6
DANN	Benign	0.72
PhyloP100		1.6
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: rs5946040; hg19: chrX-114247766;