rs3771166

Variant summary

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

The NM_003855.5(IL18R1):​c.302+1694G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,054 control chromosomes in the GnomAD database, including 16,448 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 0.44 ( 16448 hom., cov: 33)

Consequence

IL18R1
NM_003855.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21
Variant links:
Genes affected
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]

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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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL18R1NM_003855.5 linkuse as main transcriptc.302+1694G>A intron_variant ENST00000233957.7 NP_003846.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL18R1ENST00000233957.7 linkuse as main transcriptc.302+1694G>A intron_variant 5 NM_003855.5 ENSP00000233957 P1
IL18R1ENST00000409599.5 linkuse as main transcriptc.302+1694G>A intron_variant 5 ENSP00000387211 P1
IL18R1ENST00000410040.5 linkuse as main transcriptc.302+1694G>A intron_variant 2 ENSP00000386663
IL18R1ENST00000677287.1 linkuse as main transcriptc.302+1694G>A intron_variant, NMD_transcript_variant ENSP00000503023

Frequencies

GnomAD3 genomes
AF:
0.439
AC:
66727
AN:
151936
Hom.:
16423
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.658
Gnomad AMI
AF:
0.404
Gnomad AMR
AF:
0.315
Gnomad ASJ
AF:
0.476
Gnomad EAS
AF:
0.128
Gnomad SAS
AF:
0.201
Gnomad FIN
AF:
0.424
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.378
Gnomad OTH
AF:
0.405
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.439
AC:
66801
AN:
152054
Hom.:
16448
Cov.:
33
AF XY:
0.433
AC XY:
32190
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.658
Gnomad4 AMR
AF:
0.314
Gnomad4 ASJ
AF:
0.476
Gnomad4 EAS
AF:
0.129
Gnomad4 SAS
AF:
0.200
Gnomad4 FIN
AF:
0.424
Gnomad4 NFE
AF:
0.377
Gnomad4 OTH
AF:
0.402
Alfa
AF:
0.372
Hom.:
23418
Bravo
AF:
0.444
Asia WGS
AF:
0.179
AC:
623
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
0.58
DANN
Benign
0.38

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

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

Other links and lift over

dbSNP: rs3771166; hg19: chr2-102986222; COSMIC: COSV52123359; API