rs360721
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001562.4(IL18):c.-8-132C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000356 in 534,296 control chromosomes in the GnomAD database, including 1 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 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000039 ( 1 hom. )
Consequence
IL18
NM_001562.4 intron
NM_001562.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.00
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 made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL18 | NM_001562.4 | c.-8-132C>T | intron_variant | ENST00000280357.12 | NP_001553.1 | |||
IL18 | NM_001243211.2 | c.-8-132C>T | intron_variant | NP_001230140.1 | ||||
IL18 | NM_001386420.1 | c.-29-111C>T | intron_variant | NP_001373349.1 | ||||
IL18 | XM_011542805.2 | c.-29-111C>T | intron_variant | XP_011541107.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL18 | ENST00000280357.12 | c.-8-132C>T | intron_variant | 1 | NM_001562.4 | ENSP00000280357 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151938Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000392 AC: 15AN: 382240Hom.: 1 AF XY: 0.0000653 AC XY: 13AN XY: 199070
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74306
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at