Genetic Variant IL13RA1:c.*964T>G (chrX-118792818-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.641

Publications

8 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13RA1	NM_001560.3 link	c.*964T>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000371666.8	NP_001551.1	P78552-1
IL13RA1	XM_047442096.1 link	c.1192-12114T>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.*964T>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_001560.3	ENSP00000360730.3		P78552-1
IL13RA1	ENST00000652600.1 link	c.*964T>G		3_prime_UTR_variant	Exon 12 of 12			ENSP00000498980.1		A0A494C1C4

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

18702

AN:

111026

Hom.:

1457

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.300

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.168

AC:

18711

AN:

111078

Hom.:

1456

Cov.:

AF XY:

0.176

AC XY:

5853

AN XY:

33292

show subpopulations

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:

AN:

214

European-Non Finnish (NFE)

AF:

0.159

AC:

8426

AN:

52957

Other (OTH)

AF:

0.208

AC:

317

AN:

1522

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

519

1038

1556

2075

2594

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.172

Hom.:

7813

Bravo

AF:

0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.1

(source)

DANN

Benign

0.56

PhyloP100

0.64

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over