NM_000877.4:c.-83-1028G>T

Variant names:

• chr2-102152913-G-T
• rs2192752
• NM_000877.4:c.-83-1028G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000877.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1R1	NM_000877.4	MANE Select	c.-83-1028G>T		intron	N/A	NP_000868.1
	IL1R1	NM_001320978.2		c.-83-1028G>T		intron	N/A	NP_001307907.1
	IL1R1	NM_001320980.2		c.-83-1028G>T		intron	N/A	NP_001307909.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1R1	ENST00000410023.6	TSL:1 MANE Select	c.-83-1028G>T		intron	N/A	ENSP00000386380.1
	IL1R1	ENST00000409929.5	TSL:1	c.-83-1028G>T		intron	N/A	ENSP00000386776.1
	IL1R1	ENST00000409288.5	TSL:5	c.-83-1028G>T		intron	N/A	ENSP00000386478.1

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

African (AFR) AF: 0.939 AC: 38938 AN: 41480

American (AMR) AF: 0.818 AC: 12499 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2754 AN: 3470

East Asian (EAS) AF: 0.858 AC: 4436 AN: 5172

South Asian (SAS) AF: 0.763 AC: 3673 AN: 4814

European-Finnish (FIN) AF: 0.878 AC: 9251 AN: 10540

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52503 AN: 67992

Other (OTH) AF: 0.804 AC: 1695 AN: 2108

Alfa AF: 0.793 Hom.: 119138

Bravo AF: 0.836

Asia WGS AF: 0.837 AC: 2912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.59
PhyloP100		0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2192752; hg19: chr2-102769373;