rs6543116

Variant names:

• chr2-102311266-A-G
• rs6543116
• ENST00000404917.6:c.-504A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000404917.6(IL1RL1):​c.-504A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,004 control chromosomes in the GnomAD database, including 44,579 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 0.76 (44579 hom., cov: 31)
• Consequence: IL1RL1 ENST00000404917.6 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951
• Publications: 13 publications found

Genes affected

IL1RL1 (HGNC:5998): (interleukin 1 receptor like 1) The protein encoded by this gene is a member of the interleukin 1 receptor family. Studies of the similar gene in mouse suggested that this receptor can be induced by proinflammatory stimuli, and may be involved in the function of helper T cells. This gene, interleukin 1 receptor, type I (IL1R1), interleukin 1 receptor, type II (IL1R2) and interleukin 1 receptor-like 2 (IL1RL2) form a cytokine receptor gene cluster in a region mapped to chromosome 2q12. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RL1	ENST00000404917.6	c.-504A>G		upstream_gene_variant		2		ENSP00000384822.2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115172 AN: 151886 Hom.: 44529 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.756

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.758 AC: 115274 AN: 152004 Hom.: 44579 Cov.: 31 AF XY: 0.750 AC XY: 55704 AN XY: 74272

African (AFR) AF: 0.874 AC: 36240 AN: 41482

American (AMR) AF: 0.596 AC: 9079 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2713 AN: 3472

East Asian (EAS) AF: 0.567 AC: 2935 AN: 5172

South Asian (SAS) AF: 0.561 AC: 2703 AN: 4822

European-Finnish (FIN) AF: 0.736 AC: 7761 AN: 10538

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51403 AN: 67958

Other (OTH) AF: 0.759 AC: 1604 AN: 2114

Alfa AF: 0.727 Hom.: 9124

Bravo AF: 0.753

Asia WGS AF: 0.594 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.33
PhyloP100		-0.95
PromoterAI		0.0014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6543116; hg19: chr2-102927726;