ENST00000409929.5:c.-83-35850A>G

Variant names:

• chr2-102118091-A-G
• rs1465325
• ENST00000409929.5:c.-83-35850A>G

Variant summary

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

The ENST00000409929.5(IL1R1):​c.-83-35850A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,006 control chromosomes in the GnomAD database, including 2,007 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 0.16 (2007 hom., cov: 31)
• Consequence: IL1R1 ENST00000409929.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 12 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R1	NM_001320978.2	c.-83-35850A>G		intron_variant	Intron 1 of 11		NP_001307907.1
IL1R1	NM_001320980.2	c.-84+13219A>G		intron_variant	Intron 1 of 11		NP_001307909.1
IL1R1	NM_001288706.2	c.-83-35850A>G		intron_variant	Intron 1 of 11		NP_001275635.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000409929.5	c.-83-35850A>G		intron_variant	Intron 1 of 11	1		ENSP00000386776.1
IL1R1	ENST00000409329.5	c.-84+13219A>G		intron_variant	Intron 1 of 10	5		ENSP00000387131.1
IL1R1	ENST00000424272.5	c.-83-35850A>G		intron_variant	Intron 1 of 10	5		ENSP00000415366.1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23611 AN: 151892 Hom.: 2005 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.155 AC: 23630 AN: 152006 Hom.: 2007 Cov.: 31 AF XY: 0.156 AC XY: 11615 AN XY: 74320

African (AFR) AF: 0.111 AC: 4621 AN: 41476

American (AMR) AF: 0.120 AC: 1827 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3470

East Asian (EAS) AF: 0.175 AC: 904 AN: 5164

South Asian (SAS) AF: 0.200 AC: 961 AN: 4806

European-Finnish (FIN) AF: 0.192 AC: 2025 AN: 10556

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.174 AC: 11850 AN: 67952

Other (OTH) AF: 0.149 AC: 314 AN: 2108

Alfa AF: 0.158 Hom.: 823

Bravo AF: 0.144

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.80
PhyloP100		0.039
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1465325; hg19: chr2-102734551; COSMIC: COSV68605443;