2-102355405-G-T

Variant names:

• chr2-102355405-G-T
• rs13015714
• ENST00000410040.5:c.-28-7228G>T

Variant summary

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

The ENST00000410040.5(IL18R1):​c.-28-7228G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,142 control chromosomes in the GnomAD database, including 45,767 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 0.77 (45767 hom., cov: 33)
• Consequence: IL18R1 ENST00000410040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL18R1	ENST00000410040.5	c.-28-7228G>T		intron_variant	Intron 1 of 10	2		ENSP00000386663.1

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116777 AN: 152022 Hom.: 45718 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.768 AC: 116878 AN: 152142 Hom.: 45767 Cov.: 33 AF XY: 0.762 AC XY: 56661 AN XY: 74374

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.763

Alfa AF: 0.758 Hom.: 90997

Bravo AF: 0.756

Asia WGS AF: 0.591 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13015714; hg19: chr2-102971865; COSMIC: COSV52114133;