2-102237594-C-T

Variant names:

• chr2-102237594-C-T
• rs7583215
• NM_003854.4:c.1679-1598C>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.1679-1598C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,132 control chromosomes in the GnomAD database, including 3,746 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 0.20 (3746 hom., cov: 32)
• Consequence: IL1RL2 NM_003854.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1RL2	NM_003854.4	MANE Select	c.1679-1598C>T		intron	N/A	NP_003845.2
	IL1RL2	NM_001351446.2		c.1679-1598C>T		intron	N/A	NP_001338375.1	Q9HB29-1
	IL1RL2	NM_001351447.1		c.1325-1598C>T		intron	N/A	NP_001338376.1	Q9HB29-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1RL2	ENST00000264257.7	TSL:1 MANE Select	c.1679-1598C>T		intron	N/A	ENSP00000264257.2	Q9HB29-1
	IL1RL2	ENST00000441515.3	TSL:1	c.1325-1598C>T		intron	N/A	ENSP00000413348.2	Q9HB29-2
	IL1RL2	ENST00000908896.1		c.1886-1598C>T		intron	N/A	ENSP00000578955.1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30694 AN: 152014 Hom.: 3735 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.202 AC: 30748 AN: 152132 Hom.: 3746 Cov.: 32 AF XY: 0.200 AC XY: 14889 AN XY: 74382

African (AFR) AF: 0.280 AC: 11611 AN: 41476

American (AMR) AF: 0.319 AC: 4873 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1638 AN: 5174

South Asian (SAS) AF: 0.102 AC: 491 AN: 4824

European-Finnish (FIN) AF: 0.131 AC: 1390 AN: 10572

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9867 AN: 68010

Other (OTH) AF: 0.194 AC: 409 AN: 2112

Alfa AF: 0.161 Hom.: 6523

Bravo AF: 0.226

Asia WGS AF: 0.213 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.83
PhyloP100		1.3
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: rs7583215; hg19: chr2-102854054; COSMIC: COSV51816645;