2-102141867-C-T

Variant names:

• chr2-102141867-C-T
• rs2234650
• ENST00000409929.5:c.-83-12074C>T

Variant summary

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

The NM_001320981.2(IL1R1):​c.-135C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,990 control chromosomes in the GnomAD database, including 14,829 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 0.41 (14822 hom., cov: 31)
  • Exomes 𝑓: 0.31 (7 hom.)
• Consequence: IL1R1 NM_001320981.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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 (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R1	NM_001320981.2	c.-135C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 12		NP_001307910.1
IL1R1	NM_001320981.2	c.-135C>T		5_prime_UTR_variant	Exon 1 of 12		NP_001307910.1
IL1R1	NM_001320978.2	c.-83-12074C>T		intron_variant	Intron 1 of 11		NP_001307907.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000409929.5	c.-83-12074C>T		intron_variant	Intron 1 of 11	1		ENSP00000386776.1
IL1R1	ENST00000428279	c.-581C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 11	5		ENSP00000410461.1
IL1R1	ENST00000450319	c.-135C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 5	3		ENSP00000411627.1

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62886 AN: 151792 Hom.: 14799 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.396

GnomAD4 exome AF: 0.313 AC: 25 AN: 80 Hom.: 7 Cov.: 0 AF XY: 0.271 AC XY: 13 AN XY: 48

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.415 AC: 62970 AN: 151910 Hom.: 14822 Cov.: 31 AF XY: 0.411 AC XY: 30528 AN XY: 74230

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.393

Alfa AF: 0.355 Hom.: 1297

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	-0.82
CADD	Benign	2.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2234650; hg19: chr2-102758327; COSMIC: COSV68605532; COSMIC: COSV68605532;