NM_001560.3:c.1107-1095C>G

Variant names:

• chrX-118775332-C-G
• rs2265753
• NM_001560.3:c.1107-1095C>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.1107-1095C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 110,066 control chromosomes in the GnomAD database, including 4,310 homozygotes. There are 9,465 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 0.29 (4310 hom., 9465 hem., cov: 22)
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 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.1107-1095C>G		intron	N/A	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.1107-1095C>G		intron	N/A	ENSP00000360730.3	P78552-1
	IL13RA1	ENST00000965042.1		c.1248-1095C>G		intron	N/A	ENSP00000635101.1
	IL13RA1	ENST00000865793.1		c.1107-1095C>G		intron	N/A	ENSP00000535852.1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 32126 AN: 110014 Hom.: 4310 Cov.: 22

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.0453

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.292 AC: 32146 AN: 110066 Hom.: 4310 Cov.: 22 AF XY: 0.292 AC XY: 9465 AN XY: 32372

African (AFR) AF: 0.483 AC: 14552 AN: 30113

American (AMR) AF: 0.417 AC: 4281 AN: 10265

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 659 AN: 2627

East Asian (EAS) AF: 0.448 AC: 1549 AN: 3457

South Asian (SAS) AF: 0.323 AC: 837 AN: 2592

European-Finnish (FIN) AF: 0.198 AC: 1149 AN: 5800

Middle Eastern (MID) AF: 0.357 AC: 76 AN: 213

European-Non Finnish (NFE) AF: 0.162 AC: 8536 AN: 52806

Other (OTH) AF: 0.315 AC: 476 AN: 1509

Alfa AF: 0.241 Hom.: 1465

Bravo AF: 0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.33
PhyloP100		1.0
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: rs2265753; hg19: chrX-117909295;