NM_003854.4:c.650-821C>T

Variant names:

• chr2-102211279-C-T
• rs10490570
• NM_003854.4:c.650-821C>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.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
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0585 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.650-821C>T		intron	N/A	NP_003845.2
	IL1RL2	NM_001351446.2		c.650-821C>T		intron	N/A	NP_001338375.1
	IL1RL2	NM_001351447.1		c.299-824C>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.650-821C>T		intron	N/A	ENSP00000264257.2
	IL1RL2	ENST00000441515.3	TSL:1	c.299-824C>T		intron	N/A	ENSP00000413348.2
	IL1RL2	ENST00000481806.1	TSL:5	n.312-821C>T		intron	N/A

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

African (AFR) AF: 0.0598 AC: 2481 AN: 41484

American (AMR) AF: 0.0618 AC: 944 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0653 AC: 226 AN: 3462

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0122 AC: 59 AN: 4820

European-Finnish (FIN) AF: 0.0147 AC: 155 AN: 10580

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0492 AC: 3345 AN: 68016

Other (OTH) AF: 0.0621 AC: 131 AN: 2108

Alfa AF: 0.0484 Hom.: 30

Bravo AF: 0.0552

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.036
DANN	Benign	0.66
PhyloP100		-2.6
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: rs10490570; hg19: chr2-102827739;