rs5744258

chr11-112151044-C-Gchr11-112151044-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001562.4(IL18):c.92-838G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,144 control chromosomes in the GnomAD database, including 2,692 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 0.16 (2691 hom., cov: 32)
  • Exomes 𝑓: 0.36 (1 hom.)
• Consequence: IL18 NM_001562.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL18	NM_001562.4	c.92-838G>C		intron_variant		ENST00000280357.12
IL18	NM_001243211.2	c.80-838G>C		intron_variant
IL18	NM_001386420.1	c.92-838G>C		intron_variant
IL18	XM_011542805.2	c.80-838G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL18	ENST00000280357.12	c.92-838G>C		intron_variant		1	NM_001562.4	P3

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24688 AN: 152012 Hom.: 2690 Cov.: 32

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00538

Gnomad SAS AF: 0.0818

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.157

GnomAD4 exome AF: 0.357 AC: 5 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.375 AC XY: 3 AN XY: 8

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.417

GnomAD4 genome AF: 0.162 AC: 24687 AN: 152130 Hom.: 2691 Cov.: 32 AF XY: 0.158 AC XY: 11751 AN XY: 74340

Gnomad4 AFR AF: 0.0454

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.00520

Gnomad4 SAS AF: 0.0823

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.155

Alfa AF: 0.0823 Hom.: 146

Bravo AF: 0.153

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	14
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.17		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

Other links and lift over

dbSNP: rs5744258; hg19: chr11-112021767;