rs2287047

Variant names:

• chr2-102157594-G-A
• rs2287047
• NM_000877.4:c.-6-125G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-102157594-G-A
• chr2-102157594-G-C
• chr2-102157594-G-T

Variant summary

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

The NM_000877.4(IL1R1):​c.-6-125G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 680,202 control chromosomes in the GnomAD database, including 41,139 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 0.38 (12498 hom., cov: 32)
  • Exomes 𝑓: 0.32 (28641 hom.)
• Consequence: IL1R1 NM_000877.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R1	NM_000877.4	c.-6-125G>A		intron_variant	Intron 2 of 11	ENST00000410023.6	NP_000868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000410023.6	c.-6-125G>A		intron_variant	Intron 2 of 11	1	NM_000877.4	ENSP00000386380.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58250 AN: 151934 Hom.: 12478 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.358

GnomAD4 exome AF: 0.320 AC: 168816 AN: 528150 Hom.: 28641 AF XY: 0.319 AC XY: 91319 AN XY: 286324

Gnomad4 AFR exome AF: 0.587

Gnomad4 AMR exome AF: 0.278

Gnomad4 ASJ exome AF: 0.395

Gnomad4 EAS exome AF: 0.481

Gnomad4 SAS exome AF: 0.309

Gnomad4 FIN exome AF: 0.264

Gnomad4 NFE exome AF: 0.298

Gnomad4 OTH exome AF: 0.331

GnomAD4 genome AF: 0.384 AC: 58327 AN: 152052 Hom.: 12498 Cov.: 32 AF XY: 0.381 AC XY: 28322 AN XY: 74336

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.354

Alfa AF: 0.326 Hom.: 4850

Bravo AF: 0.396

Asia WGS AF: 0.374 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.34

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: rs2287047; hg19: chr2-102774054; COSMIC: COSV52105345;