2-102343547-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003856.4(IL1RL1):c.*115G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000192 in 1,565,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
IL1RL1
NM_003856.4 3_prime_UTR
NM_003856.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.638
Publications
27 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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003856.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| IL1RL1 | NM_016232.5 | MANE Select | c.970+132G>T | intron | N/A | NP_057316.3 | |||
| IL1RL1 | NM_003856.4 | c.*115G>T | 3_prime_UTR | Exon 8 of 8 | NP_003847.2 | ||||
| IL1RL1 | NM_001282408.2 | c.*115G>T | 3_prime_UTR | Exon 7 of 7 | NP_001269337.1 | Q01638-4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| IL1RL1 | ENST00000311734.6 | TSL:1 | c.*115G>T | 3_prime_UTR | Exon 8 of 8 | ENSP00000310371.2 | Q01638-2 | ||
| IL1RL1 | ENST00000233954.6 | TSL:1 MANE Select | c.970+132G>T | intron | N/A | ENSP00000233954.1 | Q01638-1 | ||
| IL1RL1 | ENST00000427077.1 | TSL:1 | n.*492G>T | non_coding_transcript_exon | Exon 9 of 9 | ENSP00000391120.1 | Q01638-3 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 152050Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152050
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000142 AC: 2AN: 1413166Hom.: 0 Cov.: 34 AF XY: 0.00000143 AC XY: 1AN XY: 698484 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1413166
Hom.:
Cov.:
34
AF XY:
AC XY:
1
AN XY:
698484
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32558
American (AMR)
AF:
AC:
0
AN:
41126
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23564
East Asian (EAS)
AF:
AC:
0
AN:
39276
South Asian (SAS)
AF:
AC:
0
AN:
79628
European-Finnish (FIN)
AF:
AC:
0
AN:
42810
Middle Eastern (MID)
AF:
AC:
0
AN:
4994
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1090582
Other (OTH)
AF:
AC:
0
AN:
58628
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000658 AC: 1AN: 152050Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74262 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152050
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74262
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41422
American (AMR)
AF:
AC:
0
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5170
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10576
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67994
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.