rs3732131

Variant names:

• chr2-102178143-A-G
• rs3732131
• NM_000877.4:c.*1384A>G

Variant summary

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

The NM_000877.4(IL1R1):​c.*1384A>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 0.124 in 152,526 control chromosomes in the GnomAD database, including 1,712 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 0.12 (1711 hom., cov: 32)
  • Exomes 𝑓: 0.068 (1 hom.)
• Consequence: IL1R1 NM_000877.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

IL1R1 (HGNC:5993): (interleukin 1 receptor type 1) This gene encodes a cytokine receptor that belongs to the interleukin-1 receptor family. The encoded protein is a receptor for interleukin-1 alpha, interleukin-1 beta, and interleukin-1 receptor antagonist. It is an important mediator involved in many cytokine-induced immune and inflammatory responses. This gene is located in a cluster of related cytokine receptor genes on chromosome 2q12. [provided by RefSeq, Dec 2013]

IL1R1-AS1 (HGNC:53898): (IL1R1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R1	NM_000877.4	c.*1384A>G		3_prime_UTR_variant	Exon 12 of 12	ENST00000410023.6	NP_000868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000410023.6	c.*1384A>G		3_prime_UTR_variant	Exon 12 of 12	1	NM_000877.4	ENSP00000386380.1
IL1R1	ENST00000409589.5	c.*906A>G		3_prime_UTR_variant	Exon 6 of 6	5		ENSP00000386555.1
IL1R1-AS1	ENST00000428188.1	n.305+1769T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18793 AN: 152084 Hom.: 1698 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.0679 AC: 22 AN: 324 Hom.: 1 Cov.: 0 AF XY: 0.0693 AC XY: 14 AN XY: 202

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0643

Gnomad4 FIN exome AF: 0.0806

Gnomad4 NFE exome AF: 0.0784

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.124 AC: 18824 AN: 152202 Hom.: 1711 Cov.: 32 AF XY: 0.125 AC XY: 9281 AN XY: 74412

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.0409

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.0664

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0948 Hom.: 1596

Bravo AF: 0.148

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.52

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: rs3732131; hg19: chr2-102794603;