NM_003854.4:c.490-3074T>C

Variant names:

• chr2-102198482-T-C
• rs870684
• NM_003854.4:c.490-3074T>C

Variant summary

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

The NM_003854.4(IL1RL2):​c.490-3074T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,018 control chromosomes in the GnomAD database, including 6,337 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 0.27 (6337 hom., cov: 31)
• Consequence: IL1RL2 NM_003854.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 6 publications found

Genes affected

IL1RL2 (HGNC:5999): (interleukin 1 receptor like 2) The protein encoded by this gene is a member of the interleukin 1 receptor family. An experiment with transient gene expression demonstrated that this receptor was incapable of binding to interleukin 1 alpha and interleukin 1 beta with high affinity. This gene and four other interleukin 1 receptor family genes, including interleukin 1 receptor, type I (IL1R1), interleukin 1 receptor, type II (IL1R2), interleukin 1 receptor-like 1 (IL1RL1), and interleukin 18 receptor 1 (IL18R1), form a cytokine receptor gene cluster in a region mapped to chromosome 2q12. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RL2	NM_003854.4	c.490-3074T>C		intron_variant	Intron 4 of 11	ENST00000264257.7	NP_003845.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RL2	ENST00000264257.7	c.490-3074T>C		intron_variant	Intron 4 of 11	1	NM_003854.4	ENSP00000264257.2
IL1RL2	ENST00000441515.3	c.139-3074T>C		intron_variant	Intron 2 of 9	1		ENSP00000413348.2
IL1RL2	ENST00000421464.1	c.490-3074T>C		intron_variant	Intron 4 of 4	5		ENSP00000387611.1
IL1RL2	ENST00000481806.1	n.152-3074T>C		intron_variant	Intron 2 of 9	5

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40469 AN: 151902 Hom.: 6335 Cov.: 31

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.266 AC: 40473 AN: 152018 Hom.: 6337 Cov.: 31 AF XY: 0.269 AC XY: 19993 AN XY: 74258

African (AFR) AF: 0.0949 AC: 3938 AN: 41506

American (AMR) AF: 0.243 AC: 3710 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 967 AN: 3464

East Asian (EAS) AF: 0.383 AC: 1973 AN: 5148

South Asian (SAS) AF: 0.376 AC: 1806 AN: 4806

European-Finnish (FIN) AF: 0.348 AC: 3676 AN: 10554

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23386 AN: 67950

Other (OTH) AF: 0.277 AC: 585 AN: 2110

Alfa AF: 0.289 Hom.: 1095

Bravo AF: 0.249

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-1.0
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: rs870684; hg19: chr2-102814942;