chr11-112160357-G-C
Variant names:
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
NM_001562.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.271
Publications
22 publications found
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]
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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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 140230Hom.: 0 Cov.: 27
GnomAD3 genomes
AF:
AC:
0
AN:
140230
Hom.:
Cov.:
27
Gnomad AFR
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Gnomad ASJ
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Gnomad OTH
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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: 0AN: 140230Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 67260
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
140230
Hom.:
Cov.:
27
AF XY:
AC XY:
0
AN XY:
67260
African (AFR)
AF:
AC:
0
AN:
37322
American (AMR)
AF:
AC:
0
AN:
13650
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3404
East Asian (EAS)
AF:
AC:
0
AN:
4432
South Asian (SAS)
AF:
AC:
0
AN:
4254
European-Finnish (FIN)
AF:
AC:
0
AN:
8146
Middle Eastern (MID)
AF:
AC:
0
AN:
264
European-Non Finnish (NFE)
AF:
AC:
0
AN:
65972
Other (OTH)
AF:
AC:
0
AN:
1902
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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