X-155999338-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002186.3(IL9R):​c.28+1551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,798 control chromosomes in the GnomAD database, including 19,769 homozygotes. There are 35,903 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 0.48 ( 19769 hom., 35903 hem., cov: 31)

Consequence

IL9R
NM_002186.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.248
Variant links:
Genes affected
IL9R (HGNC:6030): (interleukin 9 receptor) The protein encoded by this gene is a cytokine receptor that specifically mediates the biological effects of interleukin 9 (IL9). The functional IL9 receptor complex requires this protein as well as the interleukin 2 receptor, gamma (IL2RG), a common gamma subunit shared by the receptors of many different cytokines. The ligand binding of this receptor leads to the activation of various JAK kinases and STAT proteins, which connect to different biologic responses. This gene is located at the pseudoautosomal regions of X and Y chromosomes. Genetic studies suggested an association of this gene with the development of asthma. Multiple pseudogenes on chromosome 9, 10, 16, and 18 have been described. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL9RNM_002186.3 linkuse as main transcriptc.28+1551G>A intron_variant ENST00000244174.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL9RENST00000244174.11 linkuse as main transcriptc.28+1551G>A intron_variant 1 NM_002186.3 P1Q01113-1
IL9RENST00000369423.7 linkuse as main transcriptc.44+1551G>A intron_variant 1 Q01113-3
IL9RENST00000489233.6 linkuse as main transcriptn.54+1551G>A intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.479
AC:
72679
AN:
151678
Hom.:
19736
Cov.:
31
AF XY:
0.484
AC XY:
35809
AN XY:
74006
show subpopulations
Gnomad AFR
AF:
0.724
Gnomad AMI
AF:
0.350
Gnomad AMR
AF:
0.370
Gnomad ASJ
AF:
0.432
Gnomad EAS
AF:
0.626
Gnomad SAS
AF:
0.539
Gnomad FIN
AF:
0.574
Gnomad MID
AF:
0.429
Gnomad NFE
AF:
0.331
Gnomad OTH
AF:
0.427
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.479
AC:
72758
AN:
151798
Hom.:
19769
Cov.:
31
AF XY:
0.484
AC XY:
35903
AN XY:
74134
show subpopulations
Gnomad4 AFR
AF:
0.724
Gnomad4 AMR
AF:
0.370
Gnomad4 ASJ
AF:
0.432
Gnomad4 EAS
AF:
0.626
Gnomad4 SAS
AF:
0.538
Gnomad4 FIN
AF:
0.574
Gnomad4 NFE
AF:
0.331
Gnomad4 OTH
AF:
0.422
Bravo
AF:
0.474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.80
DANN
Benign
0.27

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs731476; hg19: chrX-155229003; API