rs997049

chr2-102165973-T-Achr2-102165973-T-G

Variant summary

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

The NM_000877.4(IL1R1):c.487-140T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 638,552 control chromosomes in the GnomAD database, including 43,249 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 0.31 (8188 hom., cov: 32)
  • Exomes 𝑓: 0.37 (35061 hom.)
• Consequence: IL1R1 NM_000877.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1R1	NM_000877.4	c.487-140T>A		intron_variant		ENST00000410023.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1R1	ENST00000410023.6	c.487-140T>A		intron_variant		1	NM_000877.4	P1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47328 AN: 151926 Hom.: 8187 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.323

GnomAD4 exome AF: 0.373 AC: 181369 AN: 486508 Hom.: 35061 AF XY: 0.373 AC XY: 94265 AN XY: 253036

Gnomad4 AFR exome AF: 0.145

Gnomad4 AMR exome AF: 0.252

Gnomad4 ASJ exome AF: 0.316

Gnomad4 EAS exome AF: 0.377

Gnomad4 SAS exome AF: 0.360

Gnomad4 FIN exome AF: 0.403

Gnomad4 NFE exome AF: 0.391

Gnomad4 OTH exome AF: 0.360

GnomAD4 genome AF: 0.311 AC: 47333 AN: 152044 Hom.: 8188 Cov.: 32 AF XY: 0.312 AC XY: 23184 AN XY: 74324

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.328

Alfa AF: 0.358 Hom.: 1412

Bravo AF: 0.295

Asia WGS AF: 0.391 AC: 1357 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.0
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: rs997049; hg19: chr2-102782433;