rs10490570

Positions:

• chr2-102211279-C-T

Variant summary

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

The NM_003854.4(IL1RL2):​c.650-821C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0496 in 152,130 control chromosomes in the GnomAD database, including 212 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 0.050 (212 hom., cov: 32)
• Consequence: IL1RL2 NM_003854.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1RL2	NM_003854.4	c.650-821C>T		intron_variant		ENST00000264257.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1RL2	ENST00000264257.7	c.650-821C>T		intron_variant		1	NM_003854.4	P1
IL1RL2	ENST00000441515.3	c.299-824C>T		intron_variant		1
IL1RL2	ENST00000481806.1	n.312-821C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0496 AC: 7533 AN: 152012 Hom.: 213 Cov.: 32

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0619

Gnomad ASJ AF: 0.0653

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0492

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0496 AC: 7541 AN: 152130 Hom.: 212 Cov.: 32 AF XY: 0.0481 AC XY: 3578 AN XY: 74384

Gnomad4 AFR AF: 0.0598

Gnomad4 AMR AF: 0.0618

Gnomad4 ASJ AF: 0.0653

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.0147

Gnomad4 NFE AF: 0.0492

Gnomad4 OTH AF: 0.0621

Alfa AF: 0.0479 Hom.: 27

Bravo AF: 0.0552

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.036
DANN	Benign	0.66

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: rs10490570; hg19: chr2-102827739;