rs3917318

Positions:

• chr2-102176300-A-G
• chr2-102176300-A-T

Variant summary

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

The NM_000877.4(IL1R1):​c.1304-53A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,519,602 control chromosomes in the GnomAD database, including 73,719 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 (7699 hom., cov: 33)
  • Exomes 𝑓: 0.30 (66020 hom.)
• Consequence: IL1R1 NM_000877.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1R1	NM_000877.4	c.1304-53A>G		intron_variant		ENST00000410023.6
IL1R1-AS1	NR_174960.1	n.306-3603T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1R1	ENST00000410023.6	c.1304-53A>G		intron_variant		1	NM_000877.4	P1
IL1R1-AS1	ENST00000428188.1	n.306-3603T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47483 AN: 152036 Hom.: 7684 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.302 AC: 412696 AN: 1367448 Hom.: 66020 Cov.: 20 AF XY: 0.302 AC XY: 205172 AN XY: 679252

Gnomad4 AFR exome AF: 0.292

Gnomad4 AMR exome AF: 0.527

Gnomad4 ASJ exome AF: 0.356

Gnomad4 EAS exome AF: 0.545

Gnomad4 SAS exome AF: 0.318

Gnomad4 FIN exome AF: 0.355

Gnomad4 NFE exome AF: 0.280

Gnomad4 OTH exome AF: 0.299

GnomAD4 genome AF: 0.312 AC: 47534 AN: 152154 Hom.: 7699 Cov.: 33 AF XY: 0.316 AC XY: 23503 AN XY: 74374

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.303

Alfa AF: 0.295 Hom.: 3195

Bravo AF: 0.317

Asia WGS AF: 0.392 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.80

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: rs3917318; hg19: chr2-102792760; COSMIC: COSV52105408; COSMIC: COSV52105408;