rs950880

Variant names:

• chr2-102316102-C-A
• rs950880
• NM_016232.5:c.-150+4479C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-102316102-C-A
• chr2-102316102-C-G
• chr2-102316102-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016232.5(IL1RL1):​c.-150+4479C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,022 control chromosomes in the GnomAD database, including 7,874 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 0.31 (7874 hom., cov: 32)
• Consequence: IL1RL1 NM_016232.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 43 publications found

Genes affected

IL1RL1 (HGNC:5998): (interleukin 1 receptor like 1) The protein encoded by this gene is a member of the interleukin 1 receptor family. Studies of the similar gene in mouse suggested that this receptor can be induced by proinflammatory stimuli, and may be involved in the function of helper T cells. This gene, interleukin 1 receptor, type I (IL1R1), interleukin 1 receptor, type II (IL1R2) and interleukin 1 receptor-like 2 (IL1RL2) form a cytokine receptor gene cluster in a region mapped to chromosome 2q12. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

IL18R1 (HGNC:5988): (interleukin 18 receptor 1) The protein encoded by this gene is a cytokine receptor that belongs to the interleukin 1 receptor family. This receptor specifically binds interleukin 18 (IL18), and is essential for IL18 mediated signal transduction. IFN-alpha and IL12 are reported to induce the expression of this receptor in NK and T cells. This gene along with four other members of the interleukin 1 receptor family, including IL1R2, IL1R1, ILRL2 (IL-1Rrp2), and IL1RL1 (T1/ST2), form a gene cluster on chromosome 2q. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RL1	NM_016232.5	c.-150+4479C>A		intron_variant	Intron 1 of 10	ENST00000233954.6	NP_057316.3
IL1RL1	NM_001282408.2	c.-147+4479C>A		intron_variant	Intron 1 of 6		NP_001269337.1
IL1RL1	XM_011512151.2	c.-150+4479C>A		intron_variant	Intron 1 of 7		XP_011510453.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RL1	ENST00000233954.6	c.-150+4479C>A		intron_variant	Intron 1 of 10	1	NM_016232.5	ENSP00000233954.1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46527 AN: 151904 Hom.: 7873 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.306 AC: 46548 AN: 152022 Hom.: 7874 Cov.: 32 AF XY: 0.305 AC XY: 22650 AN XY: 74290

African (AFR) AF: 0.165 AC: 6843 AN: 41468

American (AMR) AF: 0.277 AC: 4233 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3468

East Asian (EAS) AF: 0.438 AC: 2266 AN: 5174

South Asian (SAS) AF: 0.366 AC: 1765 AN: 4820

European-Finnish (FIN) AF: 0.320 AC: 3371 AN: 10548

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25868 AN: 67948

Other (OTH) AF: 0.347 AC: 732 AN: 2112

Alfa AF: 0.345 Hom.: 16472

Bravo AF: 0.294

Asia WGS AF: 0.412 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		0.042
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: rs950880; hg19: chr2-102932562;