rs1997502

Positions:

• chr2-102227789-A-G
• chr2-102227789-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1RL2	NM_003854.4	c.1135+1748A>G		intron_variant		ENST00000264257.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1RL2	ENST00000264257.7	c.1135+1748A>G		intron_variant		1	NM_003854.4	P1
IL1RL2	ENST00000441515.3	c.781+1748A>G		intron_variant		1
IL1RL2	ENST00000481806.1	n.797+1748A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.746

Alfa AF: 0.681 Hom.: 21735

Bravo AF: 0.780

Asia WGS AF: 0.683 AC: 2374 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	0.020
DANN	Benign	0.43

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: rs1997502; hg19: chr2-102844249;