rs16924144

Variant summary

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

The NM_033439.4(IL33):​c.-12+5394T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,102 control chromosomes in the GnomAD database, including 7,225 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 0.29 ( 7225 hom., cov: 32)

Consequence

IL33
NM_033439.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL33NM_033439.4 linkc.-12+5394T>C intron_variant Intron 1 of 7 ENST00000682010.1 NP_254274.1 O95760-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL33ENST00000682010.1 linkc.-12+5394T>C intron_variant Intron 1 of 7 NM_033439.4 ENSP00000507310.1 O95760-1
IL33ENST00000417746.6 linkc.-12+5394T>C intron_variant Intron 1 of 4 2 ENSP00000394039.2 O95760-4

Frequencies

GnomAD3 genomes
AF:
0.291
AC:
44299
AN:
151984
Hom.:
7219
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.153
Gnomad AMI
AF:
0.374
Gnomad AMR
AF:
0.368
Gnomad ASJ
AF:
0.294
Gnomad EAS
AF:
0.317
Gnomad SAS
AF:
0.375
Gnomad FIN
AF:
0.326
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.343
Gnomad OTH
AF:
0.314
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.291
AC:
44303
AN:
152102
Hom.:
7225
Cov.:
32
AF XY:
0.295
AC XY:
21911
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.153
Gnomad4 AMR
AF:
0.368
Gnomad4 ASJ
AF:
0.294
Gnomad4 EAS
AF:
0.317
Gnomad4 SAS
AF:
0.375
Gnomad4 FIN
AF:
0.326
Gnomad4 NFE
AF:
0.343
Gnomad4 OTH
AF:
0.315
Alfa
AF:
0.334
Hom.:
10345
Bravo
AF:
0.289
Asia WGS
AF:
0.339
AC:
1178
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
6.1
DANN
Benign
0.87

Splicing

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: rs16924144; hg19: chr9-6221246; COSMIC: COSV70307196; API