dbSNP rs12905: IL1RL1:c.*115G>A (chr2-102343547-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003856.4(IL1RL1):c.*115G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,564,902 control chromosomes in the GnomAD database, including 59,315 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 0.22 ( 4269 hom., cov: 33)

Exomes 𝑓: 0.28 ( 55046 hom. )

Consequence

IL1RL1
NM_003856.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.638

Variant links:

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]

IL1RL1 links:

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]

IL18R1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RL1	NM_016232.5 link	c.970+132G>A		intron_variant	Intron 8 of 10	ENST00000233954.6	NP_057316.3	Q01638-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RL1	ENST00000233954.6 link	c.970+132G>A		intron_variant	Intron 8 of 10	1	NM_016232.5	ENSP00000233954.1		Q01638-1

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33119

AN:

152028

Hom.:

4268

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0971

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.180

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.393

Gnomad SAS

AF:

0.277

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.211

GnomAD4 exome

AF:

0.275

AC:

388876

AN:

1412756

Hom.:

55046

Cov.:

AF XY:

0.276

AC XY:

192699

AN XY:

698234

show subpopulations

Gnomad4 AFR exome

AF:

0.0870

Gnomad4 AMR exome

AF:

0.163

Gnomad4 ASJ exome

AF:

0.153

Gnomad4 EAS exome

AF:

0.387

Gnomad4 SAS exome

AF:

0.283

Gnomad4 FIN exome

AF:

0.272

Gnomad4 NFE exome

AF:

0.285

Gnomad4 OTH exome

AF:

0.260

GnomAD4 genome

AF:

0.218

AC:

33126

AN:

152146

Hom.:

4269

Cov.:

AF XY:

0.218

AC XY:

16183

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.0969

Gnomad4 AMR

AF:

0.180

Gnomad4 ASJ

AF:

0.151

Gnomad4 EAS

AF:

0.394

Gnomad4 SAS

AF:

0.278

Gnomad4 FIN

AF:

0.264

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.218

Alfa

AF:

0.218

Hom.:

1452

Bravo

AF:

0.204

Asia WGS

AF:

0.339

AC:

1181

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.10

DANN

Benign

0.47

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over