rs5744276

Variant names:

• chr11-112146148-C-G
• rs5744276
• NM_001562.4:c.361-2331G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001562.4(IL18):​c.361-2331G>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 151,180 control chromosomes in the GnomAD database, including 2,671 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 (2671 hom., cov: 28)
• Consequence: IL18 NM_001562.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 7 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]

ENSG00000255292 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001562.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL18	NM_001562.4	MANE Select	c.361-2331G>C		intron	N/A	NP_001553.1	Q14116-1
	IL18	NM_001386420.1		c.361-2331G>C		intron	N/A	NP_001373349.1	Q14116-1
	IL18	NM_001243211.2		c.349-2331G>C		intron	N/A	NP_001230140.1	Q14116-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL18	ENST00000280357.12	TSL:1 MANE Select	c.361-2331G>C		intron	N/A	ENSP00000280357.7	Q14116-1
	IL18	ENST00000524595.6	TSL:1	c.349-2331G>C		intron	N/A	ENSP00000434561.1	Q14116-2
	IL18	ENST00000525547.5	TSL:1	n.1137-2331G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24565 AN: 151068 Hom.: 2670 Cov.: 28

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00544

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.157

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.162 AC: 24564 AN: 151180 Hom.: 2671 Cov.: 28 AF XY: 0.158 AC XY: 11674 AN XY: 73792

African (AFR) AF: 0.0453 AC: 1866 AN: 41198

American (AMR) AF: 0.136 AC: 2063 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 432 AN: 3462

East Asian (EAS) AF: 0.00525 AC: 27 AN: 5138

South Asian (SAS) AF: 0.0827 AC: 396 AN: 4786

European-Finnish (FIN) AF: 0.235 AC: 2425 AN: 10326

Middle Eastern (MID) AF: 0.152 AC: 44 AN: 290

European-Non Finnish (NFE) AF: 0.246 AC: 16683 AN: 67814

Other (OTH) AF: 0.155 AC: 322 AN: 2084

Alfa AF: 0.201 Hom.: 442

Bravo AF: 0.153

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.7
DANN	Benign	0.89
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5744276; hg19: chr11-112016871;