2-102344364-A-G

Variant names:

• chr2-102344364-A-G
• rs2160203
• ENST00000311734.6:c.*932A>G

Variant summary

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

The ENST00000311734.6(IL1RL1):​c.*932A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 951,648 control chromosomes in the GnomAD database, including 29,447 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 0.30 (7742 hom., cov: 32)
  • Exomes 𝑓: 0.23 (21705 hom.)
• Consequence: IL1RL1 ENST00000311734.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 19 publications found

Genes affected

IL1RL1 (HGNC:5998): (interleukin 1 receptor like 1) The protein encoded by this gene is a member of the interleukin 1 receptor family. Studies of the similar gene in mouse suggested that this receptor can be induced by proinflammatory stimuli, and may be involved in the function of helper T cells. This gene, interleukin 1 receptor, type I (IL1R1), interleukin 1 receptor, type II (IL1R2) and interleukin 1 receptor-like 2 (IL1RL2) form a cytokine receptor gene cluster in a region mapped to chromosome 2q12. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000311734.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1RL1	NM_016232.5	MANE Select	c.970+949A>G		intron	N/A	NP_057316.3
	IL1RL1	NR_104167.2		n.2319A>G		non_coding_transcript_exon	Exon 9 of 9
	IL1RL1	NM_003856.4		c.*932A>G		3_prime_UTR	Exon 8 of 8	NP_003847.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1RL1	ENST00000311734.6	TSL:1	c.*932A>G		3_prime_UTR	Exon 8 of 8	ENSP00000310371.2
	IL1RL1	ENST00000233954.6	TSL:1 MANE Select	c.970+949A>G		intron	N/A	ENSP00000233954.1
	IL1RL1	ENST00000409584.5	TSL:5	c.*932A>G		3_prime_UTR	Exon 8 of 8	ENSP00000386618.1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45153 AN: 151974 Hom.: 7729 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0956

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.275

GnomAD4 exome AF: 0.227 AC: 181402 AN: 799556 Hom.: 21705 Cov.: 14 AF XY: 0.227 AC XY: 83917 AN XY: 370162

African (AFR) AF: 0.470 AC: 6892 AN: 14670

American (AMR) AF: 0.137 AC: 131 AN: 956

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1474 AN: 4926

East Asian (EAS) AF: 0.0801 AC: 285 AN: 3556

South Asian (SAS) AF: 0.0862 AC: 1379 AN: 16006

European-Finnish (FIN) AF: 0.270 AC: 73 AN: 270

Middle Eastern (MID) AF: 0.175 AC: 273 AN: 1564

European-Non Finnish (NFE) AF: 0.226 AC: 165097 AN: 731442

Other (OTH) AF: 0.222 AC: 5798 AN: 26166

GnomAD4 genome AF: 0.297 AC: 45210 AN: 152092 Hom.: 7742 Cov.: 32 AF XY: 0.295 AC XY: 21955 AN XY: 74342

African (AFR) AF: 0.457 AC: 18955 AN: 41470

American (AMR) AF: 0.202 AC: 3081 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1085 AN: 3470

East Asian (EAS) AF: 0.0958 AC: 497 AN: 5186

South Asian (SAS) AF: 0.103 AC: 498 AN: 4820

European-Finnish (FIN) AF: 0.342 AC: 3618 AN: 10588

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16623 AN: 67994

Other (OTH) AF: 0.274 AC: 580 AN: 2116

Alfa AF: 0.250 Hom.: 7594

Bravo AF: 0.295

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.56
PhyloP100		0.37
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: rs2160203; hg19: chr2-102960824; COSMIC: COSV52113982; COSMIC: COSV52113982;