2-102236406-G-T

Variant names:

• chr2-102236406-G-T
• rs2287041
• NM_003854.4:c.1678+1129G>T

Variant summary

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

The NM_003854.4(IL1RL2):​c.1678+1129G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,922 control chromosomes in the GnomAD database, including 4,104 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 0.21 (4104 hom., cov: 32)
• Consequence: IL1RL2 NM_003854.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003854.4. 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
	IL1RL2	NM_003854.4	MANE Select	c.1678+1129G>T		intron	N/A	NP_003845.2
	IL1RL2	NM_001351446.2		c.1678+1129G>T		intron	N/A	NP_001338375.1
	IL1RL2	NM_001351447.1		c.1324+1129G>T		intron	N/A	NP_001338376.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1RL2	ENST00000264257.7	TSL:1 MANE Select	c.1678+1129G>T		intron	N/A	ENSP00000264257.2
	IL1RL2	ENST00000441515.3	TSL:1	c.1324+1129G>T		intron	N/A	ENSP00000413348.2
	IL1RL2	ENST00000481806.1	TSL:5	n.1340+1129G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31355 AN: 151804 Hom.: 4087 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.207 AC: 31422 AN: 151922 Hom.: 4104 Cov.: 32 AF XY: 0.205 AC XY: 15207 AN XY: 74282

African (AFR) AF: 0.318 AC: 13145 AN: 41358

American (AMR) AF: 0.317 AC: 4836 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1639 AN: 5142

South Asian (SAS) AF: 0.0943 AC: 455 AN: 4826

European-Finnish (FIN) AF: 0.122 AC: 1297 AN: 10592

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9142 AN: 67954

Other (OTH) AF: 0.198 AC: 416 AN: 2104

Alfa AF: 0.141 Hom.: 1052

Bravo AF: 0.234

Asia WGS AF: 0.221 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.53
PhyloP100		-1.1
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: rs2287041; hg19: chr2-102852866;