rs10521698

Variant names:

• chrX-115014860-G-T
• rs10521698
• NM_000640.3:c.247-286C>A

Variant summary

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

The NM_000640.3(IL13RA2):​c.247-286C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 110,900 control chromosomes in the GnomAD database, including 942 homozygotes. There are 4,510 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 0.15 (942 hom., 4510 hem., cov: 22)
• Consequence: IL13RA2 NM_000640.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13RA2	NM_000640.3	c.247-286C>A		intron_variant	Intron 3 of 9	ENST00000243213.2	NP_000631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL13RA2	ENST00000243213.2	c.247-286C>A		intron_variant	Intron 3 of 9	1	NM_000640.3	ENSP00000243213.1
IL13RA2	ENST00000371936.5	c.247-286C>A		intron_variant	Intron 4 of 10	5		ENSP00000361004.1
IL13RA2	ENST00000468224.1	n.551-286C>A		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.147 AC: 16293 AN: 110850 Hom.: 940 Cov.: 22

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0836

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00536

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.147 AC: 16312 AN: 110900 Hom.: 942 Cov.: 22 AF XY: 0.136 AC XY: 4510 AN XY: 33178

African (AFR) AF: 0.185 AC: 5667 AN: 30561

American (AMR) AF: 0.0835 AC: 866 AN: 10377

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 463 AN: 2635

East Asian (EAS) AF: 0.00538 AC: 19 AN: 3533

South Asian (SAS) AF: 0.115 AC: 303 AN: 2644

European-Finnish (FIN) AF: 0.101 AC: 596 AN: 5921

Middle Eastern (MID) AF: 0.181 AC: 38 AN: 210

European-Non Finnish (NFE) AF: 0.152 AC: 8052 AN: 52823

Other (OTH) AF: 0.115 AC: 176 AN: 1525

Alfa AF: 0.146 Hom.: 3051

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.060
DANN	Benign	0.33
PhyloP100		-0.65
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: rs10521698; hg19: chrX-114249423;