X-118791935-A-G

Variant names:

• chrX-118791935-A-G
• rs2495636
• NM_001560.3:c.*81A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001560.3(IL13RA1):​c.*81A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 506,868 control chromosomes in the GnomAD database, including 8,579 homozygotes. There are 32,199 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 (1510 hom., 6144 hem., cov: 23)
  • Exomes 𝑓: 0.21 (7069 hom. 26055 hem.)
• Consequence: IL13RA1 NM_001560.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 13 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13RA1	NM_001560.3	MANE Select	c.*81A>G		3_prime_UTR	Exon 11 of 11	NP_001551.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13RA1	ENST00000371666.8	TSL:1 MANE Select	c.*81A>G		3_prime_UTR	Exon 11 of 11	ENSP00000360730.3
	IL13RA1	ENST00000652600.1		c.*81A>G		3_prime_UTR	Exon 12 of 12	ENSP00000498980.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 19451 AN: 111661 Hom.: 1511 Cov.: 23

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.210 AC: 82992 AN: 395152 Hom.: 7069 Cov.: 5 AF XY: 0.225 AC XY: 26055 AN XY: 115878

African (AFR) AF: 0.0962 AC: 1048 AN: 10890

American (AMR) AF: 0.441 AC: 8389 AN: 19024

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 2729 AN: 11186

East Asian (EAS) AF: 0.439 AC: 10452 AN: 23813

South Asian (SAS) AF: 0.286 AC: 8174 AN: 28546

European-Finnish (FIN) AF: 0.202 AC: 6848 AN: 33869

Middle Eastern (MID) AF: 0.228 AC: 553 AN: 2424

European-Non Finnish (NFE) AF: 0.166 AC: 40332 AN: 243580

Other (OTH) AF: 0.205 AC: 4467 AN: 21820

GnomAD4 genome AF: 0.174 AC: 19465 AN: 111716 Hom.: 1510 Cov.: 23 AF XY: 0.181 AC XY: 6144 AN XY: 33922

African (AFR) AF: 0.0925 AC: 2852 AN: 30848

American (AMR) AF: 0.350 AC: 3676 AN: 10493

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 653 AN: 2634

East Asian (EAS) AF: 0.429 AC: 1503 AN: 3500

South Asian (SAS) AF: 0.265 AC: 707 AN: 2672

European-Finnish (FIN) AF: 0.198 AC: 1192 AN: 6027

Middle Eastern (MID) AF: 0.301 AC: 65 AN: 216

European-Non Finnish (NFE) AF: 0.159 AC: 8465 AN: 53124

Other (OTH) AF: 0.212 AC: 322 AN: 1520

Alfa AF: 0.173 Hom.: 7948

Bravo AF: 0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		1.9
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: rs2495636; hg19: chrX-117925898; COSMIC: COSV65424389;