2-102180064-A-T

Variant names:

• chr2-102180064-A-T
• rs3917332
• ENST00000428188.2:n.263-63T>A

Variant summary

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

The ENST00000428188.2(IL1R1-AS1):​n.263-63T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,086 control chromosomes in the GnomAD database, including 53,327 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 0.84 (53324 hom., cov: 30)
  • Exomes 𝑓: 0.75 (3 hom.)
• Consequence: IL1R1-AS1 ENST00000428188.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.07
• Publications: 27 publications found

Genes affected

IL1R1-AS1 (HGNC:53898): (IL1R1 antisense RNA 1)

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R1	NM_000877.4	c.*3305A>T		downstream_gene_variant		ENST00000410023.6	NP_000868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000410023.6	c.*3305A>T		downstream_gene_variant		1	NM_000877.4	ENSP00000386380.1

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127003 AN: 151954 Hom.: 53277 Cov.: 30

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.810

GnomAD4 exome AF: 0.750 AC: 9 AN: 12 Hom.: 3 AF XY: 0.750 AC XY: 6 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AF: 1.00 AC: 4 AN: 4

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.836 AC: 127103 AN: 152074 Hom.: 53324 Cov.: 30 AF XY: 0.842 AC XY: 62564 AN XY: 74330

African (AFR) AF: 0.876 AC: 36336 AN: 41464

American (AMR) AF: 0.827 AC: 12645 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2775 AN: 3470

East Asian (EAS) AF: 0.940 AC: 4856 AN: 5168

South Asian (SAS) AF: 0.835 AC: 4002 AN: 4790

European-Finnish (FIN) AF: 0.894 AC: 9463 AN: 10588

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54264 AN: 67996

Other (OTH) AF: 0.812 AC: 1714 AN: 2110

Alfa AF: 0.823 Hom.: 6406

Bravo AF: 0.834

Asia WGS AF: 0.898 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.031
DANN	Benign	0.40
PhyloP100		-5.1

Splicing

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

Other links and lift over

dbSNP: rs3917332; hg19: chr2-102796524;