NM_001560.3:c.*964T>G

Variant names:

• chrX-118792818-T-G
• rs2254672
• NM_001560.3:c.*964T>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.*964T>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 0.168 in 111,090 control chromosomes in the GnomAD database, including 1,456 homozygotes. There are 5,855 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 (1456 hom., 5853 hem., cov: 23)
  • Exomes 𝑓: 0.25 (0 hom. 2 hem.)
• Consequence: IL13RA1 NM_001560.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.641
• Publications: 8 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 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.*964T>G		3_prime_UTR	Exon 11 of 11	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.*964T>G		3_prime_UTR	Exon 11 of 11	ENSP00000360730.3	P78552-1
	IL13RA1	ENST00000865793.1		c.*964T>G		3_prime_UTR	Exon 12 of 12	ENSP00000535852.1
	IL13RA1	ENST00000865792.1		c.*964T>G		3_prime_UTR	Exon 12 of 12	ENSP00000535851.1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 18702 AN: 111026 Hom.: 1457 Cov.: 23

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.0430

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.206

GnomAD4 exome AF: 0.250 AC: 3 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.300 AC: 3 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.168 AC: 18711 AN: 111078 Hom.: 1456 Cov.: 23 AF XY: 0.176 AC XY: 5853 AN XY: 33292

African (AFR) AF: 0.0730 AC: 2236 AN: 30647

American (AMR) AF: 0.349 AC: 3648 AN: 10443

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 652 AN: 2633

East Asian (EAS) AF: 0.434 AC: 1510 AN: 3481

South Asian (SAS) AF: 0.266 AC: 697 AN: 2616

European-Finnish (FIN) AF: 0.192 AC: 1133 AN: 5891

Middle Eastern (MID) AF: 0.294 AC: 63 AN: 214

European-Non Finnish (NFE) AF: 0.159 AC: 8426 AN: 52957

Other (OTH) AF: 0.208 AC: 317 AN: 1522

Alfa AF: 0.172 Hom.: 7813

Bravo AF: 0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.56
PhyloP100		0.64
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: rs2254672; hg19: chrX-117926781;