2-102361999-C-T

Variant names:

• chr2-102361999-C-T
• rs3755276
• NM_003855.5:c.-28-634C>T

Variant summary

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

The NM_003855.5(IL18R1):​c.-28-634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,978 control chromosomes in the GnomAD database, including 16,433 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 0.44 (16433 hom., cov: 32)
• Consequence: IL18R1 NM_003855.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.35
• Publications: 21 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003855.5. 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
	IL18R1	NM_003855.5	MANE Select	c.-28-634C>T		intron	N/A	NP_003846.1	Q13478
	IL18R1	NM_001371418.1		c.-28-634C>T		intron	N/A	NP_001358347.1	B7ZKV7
	IL18R1	NM_001371419.1		c.-28-634C>T		intron	N/A	NP_001358348.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL18R1	ENST00000233957.7	TSL:5 MANE Select	c.-28-634C>T		intron	N/A	ENSP00000233957.1	Q13478
	IL18R1	ENST00000409599.5	TSL:5	c.-28-634C>T		intron	N/A	ENSP00000387211.1	Q13478
	IL18R1	ENST00000410040.5	TSL:2	c.-28-634C>T		intron	N/A	ENSP00000386663.1	Q13478

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66664 AN: 151860 Hom.: 16408 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.439 AC: 66738 AN: 151978 Hom.: 16433 Cov.: 32 AF XY: 0.433 AC XY: 32135 AN XY: 74292

African (AFR) AF: 0.658 AC: 27258 AN: 41420

American (AMR) AF: 0.313 AC: 4781 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1654 AN: 3470

East Asian (EAS) AF: 0.129 AC: 665 AN: 5172

South Asian (SAS) AF: 0.200 AC: 963 AN: 4820

European-Finnish (FIN) AF: 0.423 AC: 4465 AN: 10558

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25664 AN: 67960

Other (OTH) AF: 0.402 AC: 850 AN: 2112

Alfa AF: 0.440 Hom.: 5430

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.73
PhyloP100		-5.3
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: rs3755276; hg19: chr2-102978459;