rs4988958
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_016232.5(IL1RL1):āc.1575T>Cā(p.Ser525=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,612,504 control chromosomes in the GnomAD database, including 122,739 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: š 0.45 ( 17710 hom., cov: 30)
Exomes š: 0.37 ( 105029 hom. )
Consequence
IL1RL1
NM_016232.5 synonymous
NM_016232.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.158
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
?
Synonymous conserved (PhyloP=0.158 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1RL1 | NM_016232.5 | c.1575T>C | p.Ser525= | synonymous_variant | 11/11 | ENST00000233954.6 | |
IL1RL1 | XM_006712839.4 | c.1575T>C | p.Ser525= | synonymous_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RL1 | ENST00000233954.6 | c.1575T>C | p.Ser525= | synonymous_variant | 11/11 | 1 | NM_016232.5 | P1 | |
IL18R1 | ENST00000410040.5 | c.-28-10808T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.451 AC: 68490AN: 151754Hom.: 17681 Cov.: 30
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GnomAD3 exomes AF: 0.341 AC: 85650AN: 251140Hom.: 17296 AF XY: 0.332 AC XY: 45038AN XY: 135766
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GnomAD4 exome AF: 0.368 AC: 538094AN: 1460630Hom.: 105029 Cov.: 36 AF XY: 0.362 AC XY: 263069AN XY: 726690
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GnomAD4 genome ? AF: 0.451 AC: 68570AN: 151874Hom.: 17710 Cov.: 30 AF XY: 0.444 AC XY: 32981AN XY: 74230
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Ascending aortic dissection Other:1
association, no assertion criteria provided | case-control | Beijing Anzhen Hospital, Capital Medical University | Feb 01, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at