2-102166895-G-T

Position:

• chr2-102166895-G-T

Variant summary

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

The ENST00000410023.6(IL1R1):​c.655+614G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,882 control chromosomes in the GnomAD database, including 11,654 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 0.38 (11654 hom., cov: 31)
• Consequence: IL1R1 ENST00000410023.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1R1	NM_000877.4	c.655+614G>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.655+614G>T		intron_variant		1	NM_000877.4	ENSP00000386380	P1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57303 AN: 151764 Hom.: 11624 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.378 AC: 57384 AN: 151882 Hom.: 11654 Cov.: 31 AF XY: 0.381 AC XY: 28250 AN XY: 74236

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.339

Alfa AF: 0.290 Hom.: 3092

Bravo AF: 0.391

Asia WGS AF: 0.411 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.0
DANN	Benign	0.82

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: rs2160227; hg19: chr2-102783355; COSMIC: COSV52105390; COSMIC: COSV52105390;