rs11465660

chr2-102397854-C-Achr2-102397854-C-G

Variant summary

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

The NM_003855.5(IL18R1):c.*968C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 152,230 control chromosomes in the GnomAD database, including 538 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 0.075 (538 hom., cov: 32)
  • Exomes 𝑓: 0.098 (0 hom.)
• Consequence: IL18R1 NM_003855.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02

Genes affected

IL18R1 (HGNC:5988): (interleukin 18 receptor 1) The protein encoded by this gene is a cytokine receptor that belongs to the interleukin 1 receptor family. This receptor specifically binds interleukin 18 (IL18), and is essential for IL18 mediated signal transduction. IFN-alpha and IL12 are reported to induce the expression of this receptor in NK and T cells. This gene along with four other members of the interleukin 1 receptor family, including IL1R2, IL1R1, ILRL2 (IL-1Rrp2), and IL1RL1 (T1/ST2), form a gene cluster on chromosome 2q. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL18R1	NM_003855.5	c.*968C>A		3_prime_UTR_variant	11/11	ENST00000233957.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL18R1	ENST00000233957.7	c.*968C>A		3_prime_UTR_variant	11/11	5	NM_003855.5	P1
IL18R1	ENST00000409599.5	c.*968C>A		3_prime_UTR_variant	12/12	5		P1
IL18R1	ENST00000677287.1	c.*2138C>A		3_prime_UTR_variant, NMD_transcript_variant	11/11

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11418 AN: 152032 Hom.: 538 Cov.: 32

Gnomad AFR AF: 0.0406

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0409

Gnomad SAS AF: 0.0813

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.103

GnomAD4 exome AF: 0.0976 AC: 8 AN: 82 Hom.: 0 Cov.: 0 AF XY: 0.0800 AC XY: 4 AN XY: 50

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.118

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0751 AC: 11420 AN: 152148 Hom.: 538 Cov.: 32 AF XY: 0.0754 AC XY: 5605 AN XY: 74378

Gnomad4 AFR AF: 0.0406

Gnomad4 AMR AF: 0.0724

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0408

Gnomad4 SAS AF: 0.0824

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0382 Hom.: 32

Bravo AF: 0.0705

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.081
Dann	Benign	0.75

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

LitVar

Other links and lift over

dbSNP: rs11465660; hg19: chr2-103014314;