9-6248035-C-T

Variant summary

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

The NM_033439.4(IL33):​c.92-2439C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,732 control chromosomes in the GnomAD database, including 9,842 homozygotes. 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 0.35 ( 9842 hom., cov: 30)

Consequence

IL33
NM_033439.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.874
Variant links:
Genes affected
IL33 (HGNC:16028): (interleukin 33) The protein encoded by this gene is a cytokine that binds to the IL1RL1/ST2 receptor. The encoded protein is involved in the maturation of Th2 cells and the activation of mast cells, basophils, eosinophils and natural killer cells. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]

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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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL33NM_033439.4 linkc.92-2439C>T intron_variant ENST00000682010.1 NP_254274.1 O95760-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL33ENST00000682010.1 linkc.92-2439C>T intron_variant NM_033439.4 ENSP00000507310.1 O95760-1

Frequencies

GnomAD3 genomes
AF:
0.353
AC:
53495
AN:
151614
Hom.:
9825
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.368
Gnomad AMI
AF:
0.212
Gnomad AMR
AF:
0.463
Gnomad ASJ
AF:
0.273
Gnomad EAS
AF:
0.496
Gnomad SAS
AF:
0.404
Gnomad FIN
AF:
0.343
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.311
Gnomad OTH
AF:
0.350
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.353
AC:
53535
AN:
151732
Hom.:
9842
Cov.:
30
AF XY:
0.360
AC XY:
26671
AN XY:
74152
show subpopulations
Gnomad4 AFR
AF:
0.369
Gnomad4 AMR
AF:
0.463
Gnomad4 ASJ
AF:
0.273
Gnomad4 EAS
AF:
0.495
Gnomad4 SAS
AF:
0.404
Gnomad4 FIN
AF:
0.343
Gnomad4 NFE
AF:
0.311
Gnomad4 OTH
AF:
0.347
Alfa
AF:
0.223
Hom.:
499
Bravo
AF:
0.362
Asia WGS
AF:
0.404
AC:
1404
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.48
DANN
Benign
0.75

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: rs11792633; hg19: chr9-6248035; COSMIC: COSV67343554; API