rs956730

Positions:

• chr2-102141656-G-A
• chr2-102141656-G-T

Variant summary

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

The ENST00000409929.5(IL1R1):​c.-83-12285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,028 control chromosomes in the GnomAD database, including 14,876 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 0.42 (14875 hom., cov: 32)
  • Exomes 𝑓: 0.29 (1 hom.)
• Consequence: IL1R1 ENST00000409929.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1R1	NM_001288706.2	c.-83-12285G>A		intron_variant			NP_001275635.1
IL1R1	NM_001320978.2	c.-83-12285G>A		intron_variant			NP_001307907.1
IL1R1	NM_001320980.2	c.-83-12285G>A		intron_variant			NP_001307909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000409929.5	c.-83-12285G>A		intron_variant		1		ENSP00000386776
IL1R1	ENST00000409329.5	c.-83-12285G>A		intron_variant		5		ENSP00000387131
IL1R1	ENST00000409589.5	c.-83-12285G>A		intron_variant		5		ENSP00000386555

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63008 AN: 151872 Hom.: 14852 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.396

GnomAD4 exome AF: 0.289 AC: 11 AN: 38 Hom.: 1 AF XY: 0.273 AC XY: 6 AN XY: 22

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.415 AC: 63092 AN: 151990 Hom.: 14875 Cov.: 32 AF XY: 0.412 AC XY: 30592 AN XY: 74280

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.392

Alfa AF: 0.336 Hom.: 4662

Bravo AF: 0.428

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs956730; hg19: chr2-102758116;