rs2234650
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000409929.5(IL1R1):c.-83-12074C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
IL1R1
ENST00000409929.5 intron
ENST00000409929.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.34
Publications
40 publications found
Genes affected
IL1R1 (HGNC:5993): (interleukin 1 receptor type 1) This gene encodes a cytokine receptor that belongs to the interleukin-1 receptor family. The encoded protein is a receptor for interleukin-1 alpha, interleukin-1 beta, and interleukin-1 receptor antagonist. It is an important mediator involved in many cytokine-induced immune and inflammatory responses. This gene is located in a cluster of related cytokine receptor genes on chromosome 2q12. [provided by RefSeq, Dec 2013]
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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=-0.83).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| IL1R1 | NM_001320981.2 | c.-135C>G | 5_prime_UTR_variant | Exon 1 of 12 | NP_001307910.1 | |||
| IL1R1 | NM_001320978.2 | c.-83-12074C>G | intron_variant | Intron 1 of 11 | NP_001307907.1 | |||
| IL1R1 | NM_001320980.2 | c.-83-12074C>G | intron_variant | Intron 1 of 11 | NP_001307909.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| IL1R1 | ENST00000409929.5 | c.-83-12074C>G | intron_variant | Intron 1 of 11 | 1 | ENSP00000386776.1 | ||||
| IL1R1 | ENST00000428279.5 | c.-581C>G | 5_prime_UTR_variant | Exon 1 of 11 | 5 | ENSP00000410461.1 | ||||
| IL1R1 | ENST00000450319.5 | c.-135C>G | 5_prime_UTR_variant | Exon 1 of 5 | 3 | ENSP00000411627.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 82Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 50
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
82
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
50
African (AFR)
AF:
AC:
0
AN:
6
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
0
AN:
4
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66
Other (OTH)
AF:
AC:
0
AN:
6
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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