rs1997502

Variant names:

• chr2-102227789-A-G
• rs1997502
• NM_003854.4:c.1135+1748A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-102227789-A-G
• chr2-102227789-A-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.1135+1748A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,092 control chromosomes in the GnomAD database, including 44,526 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 0.75 (44526 hom., cov: 31)
• Consequence: IL1RL2 NM_003854.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 10 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 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.1135+1748A>G		intron	N/A	NP_003845.2
	IL1RL2	NM_001351446.2		c.1135+1748A>G		intron	N/A	NP_001338375.1
	IL1RL2	NM_001351447.1		c.781+1748A>G		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.1135+1748A>G		intron	N/A	ENSP00000264257.2
	IL1RL2	ENST00000441515.3	TSL:1	c.781+1748A>G		intron	N/A	ENSP00000413348.2
	IL1RL2	ENST00000481806.1	TSL:5	n.797+1748A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114681 AN: 151974 Hom.: 44462 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.755 AC: 114810 AN: 152092 Hom.: 44526 Cov.: 31 AF XY: 0.754 AC XY: 56037 AN XY: 74344

African (AFR) AF: 0.936 AC: 38862 AN: 41524

American (AMR) AF: 0.809 AC: 12364 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2073 AN: 3470

East Asian (EAS) AF: 0.697 AC: 3603 AN: 5168

South Asian (SAS) AF: 0.605 AC: 2915 AN: 4816

European-Finnish (FIN) AF: 0.650 AC: 6860 AN: 10552

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45665 AN: 67968

Other (OTH) AF: 0.746 AC: 1577 AN: 2114

Alfa AF: 0.683 Hom.: 35708

Bravo AF: 0.780

Asia WGS AF: 0.683 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.020
DANN	Benign	0.43
PhyloP100		-1.2
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: rs1997502; hg19: chr2-102844249;