chr11-112160357-G-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001562.4(IL18):​c.-9+3549C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 27)
Failed GnomAD Quality Control

Consequence

IL18
NM_001562.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.271

Publications

22 publications found
Variant links:
Genes affected
IL18 (HGNC:5986): (interleukin 18) The protein encoded by this gene is a proinflammatory cytokine of the IL-1 family that is constitutively found as a precursor within the cytoplasm of a variety of cells including macrophages and keratinocytes. The inactive IL-18 precursor is processed to its active form by caspase-1, and is capable of stimulating interferon gamma production, and of regulating both T helper (Th) 1 and Th2 responses. This cytokine has been implicated in the injury of different organs, and in potentially fatal conditions characterized by a cytokine storm. In humans, IL-18 gene is located on chromosome 11. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2020]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL18NM_001562.4 linkc.-9+3549C>G intron_variant Intron 1 of 5 ENST00000280357.12 NP_001553.1 Q14116-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL18ENST00000280357.12 linkc.-9+3549C>G intron_variant Intron 1 of 5 1 NM_001562.4 ENSP00000280357.7 Q14116-1
ENSG00000255292ENST00000532699.1 linkn.315-10062G>C intron_variant Intron 3 of 5 3 ENSP00000456434.1 H3BRW5

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
140230
Hom.:
0
Cov.:
27
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
140230
Hom.:
0
Cov.:
27
AF XY:
0.00
AC XY:
0
AN XY:
67260
African (AFR)
AF:
0.00
AC:
0
AN:
37322
American (AMR)
AF:
0.00
AC:
0
AN:
13650
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3404
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4432
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4254
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
8146
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
264
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
65972
Other (OTH)
AF:
0.00
AC:
0
AN:
1902
Alfa
AF:
0.00
Hom.:
2632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.61
DANN
Benign
0.41
PhyloP100
-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

Other links and lift over

dbSNP: rs795467; hg19: chr11-112031080; API