chr2-102193708-T-G

Position:

• chr2-102193708-T-G

Variant summary

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

The NM_003854.4(IL1RL2):​c.489+1588T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,266 control chromosomes in the GnomAD database, including 1,894 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 0.15 (1894 hom., cov: 34)
• Consequence: IL1RL2 NM_003854.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808

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]

IL1RL2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1RL2	NM_003854.4	c.489+1588T>G		intron_variant		ENST00000264257.7	NP_003845.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RL2	ENST00000264257.7	c.489+1588T>G		intron_variant		1	NM_003854.4	ENSP00000264257.2
IL1RL2	ENST00000441515.3	c.138+5783T>G		intron_variant		1		ENSP00000413348.2
IL1RL2	ENST00000421464.1	c.489+1588T>G		intron_variant		5		ENSP00000387611.1
IL1RL2	ENST00000481806.1	n.151+5783T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22730 AN: 152148 Hom.: 1889 Cov.: 34

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.0374

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.149 AC: 22757 AN: 152266 Hom.: 1894 Cov.: 34 AF XY: 0.147 AC XY: 10973 AN XY: 74460

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0778

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.148

Alfa AF: 0.130 Hom.: 1078

Bravo AF: 0.156

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.58

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: rs1558648; hg19: chr2-102810168;