chr2-102177822-G-A

Position:

• chr2-102177822-G-A

Variant summary

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

The NM_000877.4(IL1R1):​c.*1063G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,146 control chromosomes in the GnomAD database, including 7,295 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 0.28 (7276 hom., cov: 32)
  • Exomes 𝑓: 0.39 (19 hom.)
• Consequence: IL1R1 NM_000877.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1R1	NM_000877.4	c.*1063G>A		3_prime_UTR_variant	12/12	ENST00000410023.6	NP_000868.1
IL1R1-AS1	NR_174960.1	n.305+2090C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000410023.6	c.*1063G>A		3_prime_UTR_variant	12/12	1	NM_000877.4	ENSP00000386380	P1
IL1R1-AS1	ENST00000428188.1	n.305+2090C>T		intron_variant, non_coding_transcript_variant		3
IL1R1	ENST00000409589.5	c.*585G>A		3_prime_UTR_variant	6/6	5		ENSP00000386555

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42866 AN: 151780 Hom.: 7273 Cov.: 32

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.293

GnomAD4 exome AF: 0.391 AC: 97 AN: 248 Hom.: 19 Cov.: 0 AF XY: 0.416 AC XY: 64 AN XY: 154

Gnomad4 EAS exome AF: 0.377

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.350

Gnomad4 NFE exome AF: 0.405

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.282 AC: 42865 AN: 151898 Hom.: 7276 Cov.: 32 AF XY: 0.284 AC XY: 21081 AN XY: 74202

Gnomad4 AFR AF: 0.0850

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.298

Alfa AF: 0.348 Hom.: 12886

Bravo AF: 0.262

Asia WGS AF: 0.363 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.28
DANN	Benign	0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2110726; hg19: chr2-102794282;