rs3771175

Variant summary

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

The ENST00000311734.6(IL1RL1):​c.*318T>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 0.144 in 1,207,844 control chromosomes in the GnomAD database, including 13,524 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 0.18 ( 2687 hom., cov: 33)
Exomes 𝑓: 0.14 ( 10837 hom. )

Consequence

IL1RL1
ENST00000311734.6 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25
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]
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL1RL1NM_016232.5 linkuse as main transcriptc.970+335T>A intron_variant ENST00000233954.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL1RL1ENST00000233954.6 linkuse as main transcriptc.970+335T>A intron_variant 1 NM_016232.5 P1Q01638-1

Frequencies

GnomAD3 genomes
AF:
0.175
AC:
26656
AN:
152108
Hom.:
2681
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.264
Gnomad AMI
AF:
0.164
Gnomad AMR
AF:
0.126
Gnomad ASJ
AF:
0.214
Gnomad EAS
AF:
0.0918
Gnomad SAS
AF:
0.0724
Gnomad FIN
AF:
0.177
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.144
Gnomad OTH
AF:
0.171
GnomAD4 exome
AF:
0.140
AC:
147585
AN:
1055620
Hom.:
10837
Cov.:
32
AF XY:
0.139
AC XY:
69328
AN XY:
500148
show subpopulations
Gnomad4 AFR exome
AF:
0.276
Gnomad4 AMR exome
AF:
0.101
Gnomad4 ASJ exome
AF:
0.226
Gnomad4 EAS exome
AF:
0.107
Gnomad4 SAS exome
AF:
0.0638
Gnomad4 FIN exome
AF:
0.163
Gnomad4 NFE exome
AF:
0.139
Gnomad4 OTH exome
AF:
0.142
GnomAD4 genome
AF:
0.175
AC:
26686
AN:
152224
Hom.:
2687
Cov.:
33
AF XY:
0.174
AC XY:
12925
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.264
Gnomad4 AMR
AF:
0.126
Gnomad4 ASJ
AF:
0.214
Gnomad4 EAS
AF:
0.0920
Gnomad4 SAS
AF:
0.0723
Gnomad4 FIN
AF:
0.177
Gnomad4 NFE
AF:
0.144
Gnomad4 OTH
AF:
0.171
Alfa
AF:
0.163
Hom.:
291
Bravo
AF:
0.174
Asia WGS
AF:
0.0900
AC:
313
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.30
DANN
Benign
0.54

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: rs3771175; hg19: chr2-102960210; COSMIC: COSV52113973; COSMIC: COSV52113973; API