chr2-102152913-G-T

Position:

• chr2-102152913-G-T

Variant summary

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

The NM_000877.4(IL1R1):​c.-83-1028G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,050 control chromosomes in the GnomAD database, including 53,306 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 0.83 (53306 hom., cov: 31)
• Consequence: IL1R1 NM_000877.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1R1	NM_000877.4	c.-83-1028G>T		intron_variant		ENST00000410023.6	NP_000868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000410023.6	c.-83-1028G>T		intron_variant		1	NM_000877.4	ENSP00000386380	P1

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126687 AN: 151932 Hom.: 53241 Cov.: 31

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.834 AC: 126806 AN: 152050 Hom.: 53306 Cov.: 31 AF XY: 0.838 AC XY: 62268 AN XY: 74316

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.804

Alfa AF: 0.779 Hom.: 69868

Bravo AF: 0.836

Asia WGS AF: 0.837 AC: 2912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.59

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: rs2192752; hg19: chr2-102769373;