NM_000877.4:c.*1384A>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000877.4. 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
	IL1R1	NM_000877.4	MANE Select	c.*1384A>G		3_prime_UTR	Exon 12 of 12	NP_000868.1	P14778
	IL1R1	NM_001320978.2		c.*1384A>G		3_prime_UTR	Exon 12 of 12	NP_001307907.1	P14778
	IL1R1	NM_001320980.2		c.*1384A>G		3_prime_UTR	Exon 12 of 12	NP_001307909.1	P14778

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1R1	ENST00000410023.6	TSL:1 MANE Select	c.*1384A>G		3_prime_UTR	Exon 12 of 12	ENSP00000386380.1	P14778
	IL1R1	ENST00000853658.1		c.*1384A>G		3_prime_UTR	Exon 12 of 12	ENSP00000523717.1
	IL1R1	ENST00000853659.1		c.*1384A>G		3_prime_UTR	Exon 12 of 12	ENSP00000523718.1

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.0643 AC: 9 AN: 140

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0806 AC: 5 AN: 62

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0784 AC: 8 AN: 102

Other (OTH) AF: 0.00 AC: 0 AN: 12

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

African (AFR) AF: 0.174 AC: 7243 AN: 41510

American (AMR) AF: 0.265 AC: 4049 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0409 AC: 142 AN: 3472

East Asian (EAS) AF: 0.226 AC: 1168 AN: 5166

South Asian (SAS) AF: 0.0765 AC: 369 AN: 4822

European-Finnish (FIN) AF: 0.0664 AC: 705 AN: 10616

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0709 AC: 4819 AN: 68010

Other (OTH) AF: 0.127 AC: 269 AN: 2116

Alfa AF: 0.101 Hom.: 2179

Bravo AF: 0.148

Asia WGS AF: 0.163 AC: 567 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	1.2
DANN	Benign	0.52
PhyloP100		-0.15
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3732131;

hg19: chr2-102794603;