X-118759603-C-T

Variant names:

• chrX-118759603-C-T
• rs2997049
• NM_001560.3:c.676+1361C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001560.3(IL13RA1):​c.676+1361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.89 (30536 hom., 27718 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 3 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13RA1	NM_001560.3	c.676+1361C>T		intron_variant	Intron 5 of 10	ENST00000371666.8	NP_001551.1
IL13RA1	XM_047442096.1	c.676+1361C>T		intron_variant	Intron 5 of 10		XP_047298052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL13RA1	ENST00000371666.8	c.676+1361C>T		intron_variant	Intron 5 of 10	1	NM_001560.3	ENSP00000360730.3
IL13RA1	ENST00000371642.1	c.676+1361C>T		intron_variant	Intron 5 of 5	1		ENSP00000360705.1
IL13RA1	ENST00000652600.1	c.670+1361C>T		intron_variant	Intron 6 of 11			ENSP00000498980.1
IL13RA1	ENST00000481868.1	n.369+634C>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.887 AC: 96510 AN: 108851 Hom.: 30541 Cov.: 21

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.936

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.897

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.887 AC: 96553 AN: 108907 Hom.: 30536 Cov.: 21 AF XY: 0.890 AC XY: 27718 AN XY: 31161

African (AFR) AF: 0.914 AC: 27292 AN: 29860

American (AMR) AF: 0.921 AC: 9334 AN: 10138

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 2493 AN: 2629

East Asian (EAS) AF: 0.999 AC: 3467 AN: 3469

South Asian (SAS) AF: 0.964 AC: 2334 AN: 2422

European-Finnish (FIN) AF: 0.848 AC: 4697 AN: 5540

Middle Eastern (MID) AF: 0.939 AC: 200 AN: 213

European-Non Finnish (NFE) AF: 0.855 AC: 44843 AN: 52478

Other (OTH) AF: 0.899 AC: 1337 AN: 1488

Alfa AF: 0.871 Hom.: 68195

Bravo AF: 0.894

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.58
PhyloP100		0.53
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: rs2997049; hg19: chrX-117893566;