chrX-118750742-C-T

Variant names:

• chrX-118750742-C-T
• rs2495619
• NM_001560.3:c.488+964C>T

Variant summary

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

The NM_001560.3(IL13RA1):​c.488+964C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 109,536 control chromosomes in the GnomAD database, including 2,236 homozygotes. There are 7,248 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 0.22 (2236 hom., 7248 hem., cov: 22)
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.725
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13RA1	NM_001560.3	c.488+964C>T		intron_variant	Intron 4 of 10	ENST00000371666.8	NP_001551.1
IL13RA1	XM_047442096.1	c.488+964C>T		intron_variant	Intron 4 of 10		XP_047298052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL13RA1	ENST00000371666.8	c.488+964C>T		intron_variant	Intron 4 of 10	1	NM_001560.3	ENSP00000360730.3
IL13RA1	ENST00000371642.1	c.488+964C>T		intron_variant	Intron 4 of 5	1		ENSP00000360705.1
IL13RA1	ENST00000652600.1	c.482+964C>T		intron_variant	Intron 5 of 11			ENSP00000498980.1
IL13RA1	ENST00000481868.1	n.76+964C>T		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.224 AC: 24569 AN: 109492 Hom.: 2237 Cov.: 22

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0458

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.224 AC: 24578 AN: 109536 Hom.: 2236 Cov.: 22 AF XY: 0.228 AC XY: 7248 AN XY: 31846

African (AFR) AF: 0.254 AC: 7672 AN: 30153

American (AMR) AF: 0.377 AC: 3813 AN: 10123

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 651 AN: 2622

East Asian (EAS) AF: 0.411 AC: 1414 AN: 3440

South Asian (SAS) AF: 0.306 AC: 784 AN: 2563

European-Finnish (FIN) AF: 0.195 AC: 1096 AN: 5611

Middle Eastern (MID) AF: 0.322 AC: 69 AN: 214

European-Non Finnish (NFE) AF: 0.165 AC: 8664 AN: 52640

Other (OTH) AF: 0.257 AC: 384 AN: 1493

Alfa AF: 0.137 Hom.: 946

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.50
PhyloP100		0.72
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: rs2495619; hg19: chrX-117884705;