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rs1143627

Variant summary

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

The ENST00000418817.5(IL1B):c.-146C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 153,270 control chromosomes in the GnomAD database, including 24,871 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.56 ( 24616 hom., cov: 32)
Exomes 𝑓: 0.62 ( 255 hom. )

Consequence

IL1B
ENST00000418817.5 5_prime_UTR

Scores

2

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -0.268
Variant links:
Genes affected
IL1B (HGNC:5992): (interleukin 1 beta) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This cytokine is produced by activated macrophages as a proprotein, which is proteolytically processed to its active form by caspase 1 (CASP1/ICE). This cytokine is an important mediator of the inflammatory response, and is involved in a variety of cellular activities, including cell proliferation, differentiation, and apoptosis. The induction of cyclooxygenase-2 (PTGS2/COX2) by this cytokine in the central nervous system (CNS) is found to contribute to inflammatory pain hypersensitivity. Similarly, IL-1B has been implicated in human osteoarthritis pathogenesis. Patients with severe Coronavirus Disease 2019 (COVID-19) present elevated levels of pro-inflammatory cytokines such as IL-1B in bronchial alveolar lavage fluid samples. The lung damage induced by the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is to a large extent, a result of the inflammatory response promoted by cytokines such as IL-1B. This gene and eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. [provided by RefSeq, Jul 2020]

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=-0.56).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL1BNM_000576.3 linkuse as main transcript upstream_gene_variant ENST00000263341.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL1BENST00000263341.7 linkuse as main transcript upstream_gene_variant 1 NM_000576.3 P1

Frequencies

GnomAD3 genomes
AF:
0.556
AC:
84516
AN:
151922
Hom.:
24620
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.397
Gnomad AMI
AF:
0.736
Gnomad AMR
AF:
0.495
Gnomad ASJ
AF:
0.652
Gnomad EAS
AF:
0.530
Gnomad SAS
AF:
0.404
Gnomad FIN
AF:
0.597
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.665
Gnomad OTH
AF:
0.575
GnomAD4 exome
AF:
0.624
AC:
767
AN:
1230
Hom.:
255
Cov.:
0
AF XY:
0.614
AC XY:
387
AN XY:
630
show subpopulations
Gnomad4 AFR exome
AF:
0.250
Gnomad4 AMR exome
AF:
0.489
Gnomad4 ASJ exome
AF:
0.833
Gnomad4 EAS exome
AF:
0.667
Gnomad4 SAS exome
AF:
0.397
Gnomad4 FIN exome
AF:
0.750
Gnomad4 NFE exome
AF:
0.708
Gnomad4 OTH exome
AF:
0.655
GnomAD4 genome
AF:
0.556
AC:
84513
AN:
152040
Hom.:
24616
Cov.:
32
AF XY:
0.549
AC XY:
40793
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.396
Gnomad4 AMR
AF:
0.494
Gnomad4 ASJ
AF:
0.652
Gnomad4 EAS
AF:
0.530
Gnomad4 SAS
AF:
0.404
Gnomad4 FIN
AF:
0.597
Gnomad4 NFE
AF:
0.665
Gnomad4 OTH
AF:
0.569
Alfa
AF:
0.641
Hom.:
61214
Bravo
AF:
0.544
Asia WGS
AF:
0.443
AC:
1539
AN:
3478

ClinVar

Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Gastric cancer susceptibility after h. pylori infection Other:1
risk factor, no assertion criteria providedliterature onlyOMIMNov 04, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
11
Dann
Benign
0.91

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: rs1143627; hg19: chr2-113594387; API