rs3917289

Positions:

• chr2-102165451-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.486+147G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.076 in 449,708 control chromosomes in the GnomAD database, including 1,679 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 0.094 (846 hom., cov: 32)
  • Exomes 𝑓: 0.067 (833 hom.)
• Consequence: IL1R1 NM_000877.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.40

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1R1	NM_000877.4	c.486+147G>T		intron_variant		ENST00000410023.6	NP_000868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000410023.6	c.486+147G>T		intron_variant		1	NM_000877.4	ENSP00000386380	P1

Frequencies

GnomAD3 genomes AF: 0.0945 AC: 14372 AN: 152054 Hom.: 849 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0749

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0852

GnomAD4 exome AF: 0.0666 AC: 19819 AN: 297536 Hom.: 833 AF XY: 0.0659 AC XY: 10077 AN XY: 152924

Gnomad4 AFR exome AF: 0.143

Gnomad4 AMR exome AF: 0.0600

Gnomad4 ASJ exome AF: 0.0517

Gnomad4 EAS exome AF: 0.000169

Gnomad4 SAS exome AF: 0.0112

Gnomad4 FIN exome AF: 0.104

Gnomad4 NFE exome AF: 0.0707

Gnomad4 OTH exome AF: 0.0704

GnomAD4 genome AF: 0.0945 AC: 14376 AN: 152172 Hom.: 846 Cov.: 32 AF XY: 0.0953 AC XY: 7093 AN XY: 74416

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0748

Gnomad4 ASJ AF: 0.0589

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0765

Gnomad4 OTH AF: 0.0843

Alfa AF: 0.0773 Hom.: 309

Bravo AF: 0.0938

Asia WGS AF: 0.0170 AC: 62 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.0090
DANN	Benign	0.65

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: rs3917289; hg19: chr2-102781911;