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 151922 control chromosomes in the gnomAD Genomes database, including 24620 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 ( 24620 hom., cov: 32)
Consequence
IL1B
ENST00000418817.5 5_prime_UTR
ENST00000418817.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.268
Links
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
?
GnomAd 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 |
---|---|---|---|---|---|---|---|
IL1B | NM_000576.3 | upstream_gene_variant | ENST00000263341.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1B | ENST00000263341.7 | upstream_gene_variant | 1 | NM_000576.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.556 AC: 84516AN: 151922Hom.: 24620 Cov.: 32
GnomAD3 genomes
AF:
AC:
84516
AN:
151922
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.624 AC: 767AN: 1230Hom.: 255 AF XY: 0.614 AC XY: 387AN XY: 630
GnomAD4 exome
AF:
AC:
767
AN:
1230
Hom.:
AF XY:
AC XY:
387
AN XY:
630
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
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 provided | literature only | OMIM | Nov 04, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at