chrX-118750742-C-T

Variant summary

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

The NM_001560.3(IL13RA1):​c.488+964C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 109,536 control chromosomes in the GnomAD database, including 2,236 homozygotes. There are 7,248 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 0.22 ( 2236 hom., 7248 hem., cov: 22)

Consequence

IL13RA1
NM_001560.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.725

Publications

2 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]

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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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL13RA1NM_001560.3 linkc.488+964C>T intron_variant Intron 4 of 10 ENST00000371666.8 NP_001551.1 P78552-1
IL13RA1XM_047442096.1 linkc.488+964C>T intron_variant Intron 4 of 10 XP_047298052.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL13RA1ENST00000371666.8 linkc.488+964C>T intron_variant Intron 4 of 10 1 NM_001560.3 ENSP00000360730.3 P78552-1
IL13RA1ENST00000371642.1 linkc.488+964C>T intron_variant Intron 4 of 5 1 ENSP00000360705.1 P78552-2
IL13RA1ENST00000652600.1 linkc.482+964C>T intron_variant Intron 5 of 11 ENSP00000498980.1 A0A494C1C4
IL13RA1ENST00000481868.1 linkn.76+964C>T intron_variant Intron 1 of 5 3

Frequencies

GnomAD3 genomes
AF:
0.224
AC:
24569
AN:
109492
Hom.:
2237
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.255
Gnomad AMI
AF:
0.0458
Gnomad AMR
AF:
0.377
Gnomad ASJ
AF:
0.248
Gnomad EAS
AF:
0.410
Gnomad SAS
AF:
0.307
Gnomad FIN
AF:
0.195
Gnomad MID
AF:
0.308
Gnomad NFE
AF:
0.165
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.224
AC:
24578
AN:
109536
Hom.:
2236
Cov.:
22
AF XY:
0.228
AC XY:
7248
AN XY:
31846
show subpopulations
African (AFR)
AF:
0.254
AC:
7672
AN:
30153
American (AMR)
AF:
0.377
AC:
3813
AN:
10123
Ashkenazi Jewish (ASJ)
AF:
0.248
AC:
651
AN:
2622
East Asian (EAS)
AF:
0.411
AC:
1414
AN:
3440
South Asian (SAS)
AF:
0.306
AC:
784
AN:
2563
European-Finnish (FIN)
AF:
0.195
AC:
1096
AN:
5611
Middle Eastern (MID)
AF:
0.322
AC:
69
AN:
214
European-Non Finnish (NFE)
AF:
0.165
AC:
8664
AN:
52640
Other (OTH)
AF:
0.257
AC:
384
AN:
1493
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
642
1284
1926
2568
3210
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
266
532
798
1064
1330
<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:
0.137
Hom.:
946
Bravo
AF:
0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.0
DANN
Benign
0.50
PhyloP100
0.72
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

Publications

Other links and lift over

dbSNP: rs2495619; hg19: chrX-117884705; API