2-102178081-C-T

Position:

• chr2-102178081-C-T

Variant summary

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

The NM_000877.4(IL1R1):​c.*1322C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0505 in 152,962 control chromosomes in the GnomAD database, including 236 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 0.051 (236 hom., cov: 32)
  • Exomes 𝑓: 0.035 (0 hom.)
• Consequence: IL1R1 NM_000877.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1R1	NM_000877.4	c.*1322C>T		3_prime_UTR_variant	12/12	ENST00000410023.6	NP_000868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000410023.6	c.*1322C>T		3_prime_UTR_variant	12/12	1	NM_000877.4	ENSP00000386380.1
IL1R1	ENST00000409589.5	c.*844C>T		3_prime_UTR_variant	6/6	5		ENSP00000386555.1
IL1R1-AS1	ENST00000428188.1	n.305+1831G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0505 AC: 7689 AN: 152196 Hom.: 237 Cov.: 32

Gnomad AFR AF: 0.0648

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0185

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.0656

GnomAD4 exome AF: 0.0355 AC: 23 AN: 648 Hom.: 0 Cov.: 0 AF XY: 0.0389 AC XY: 15 AN XY: 386

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0493

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0216

Gnomad4 NFE exome AF: 0.0413

Gnomad4 OTH exome AF: 0.0455

GnomAD4 genome AF: 0.0505 AC: 7695 AN: 152314 Hom.: 236 Cov.: 32 AF XY: 0.0491 AC XY: 3659 AN XY: 74490

Gnomad4 AFR AF: 0.0647

Gnomad4 AMR AF: 0.0588

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0185

Gnomad4 NFE AF: 0.0483

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0516 Hom.: 239

Bravo AF: 0.0564

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.99
DANN	Benign	0.69

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: rs3917328; hg19: chr2-102794541;