dbSNP rs2495636: IL13RA1:c.*81A>G (chrX-118791935-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.89

Publications

13 publications found

Variant links:

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]

IL13RA1 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13RA1	NM_001560.3 link	c.*81A>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000371666.8	NP_001551.1
IL13RA1	XM_047442096.1 link	c.1192-12997A>G		intron_variant	Intron 10 of 10		XP_047298052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL13RA1	ENST00000371666.8 link	c.*81A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_001560.3	ENSP00000360730.3
IL13RA1	ENST00000652600.1 link	c.*81A>G		3_prime_UTR_variant	Exon 12 of 12			ENSP00000498980.1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

19451

AN:

111661

Hom.:

1511

Cov.:

show subpopulations

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.:

AF XY:

0.225

AC XY:

26055

AN XY:

115878

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

2034

4069

6103

8138

10172

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

684

1368

2052

2736

3420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.174

AC:

19465

AN:

111716

Hom.:

1510

Cov.:

AF XY:

0.181

AC XY:

6144

AN XY:

33922

show subpopulations

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:

AN:

216

European-Non Finnish (NFE)

AF:

0.159

AC:

8465

AN:

53124

Other (OTH)

AF:

0.212

AC:

322

AN:

1520

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

519

1037

1556

2074

2593

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.173

Hom.:

7948

Bravo

AF:

0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

1.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over