rs3771172
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003855.5(IL18R1):c.302+1284C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,070 control chromosomes in the GnomAD database, including 4,354 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.22 ( 4354 hom., cov: 33)
Consequence
IL18R1
NM_003855.5 intron
NM_003855.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.54
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=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL18R1 | NM_003855.5 | c.302+1284C>T | intron_variant | ENST00000233957.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL18R1 | ENST00000233957.7 | c.302+1284C>T | intron_variant | 5 | NM_003855.5 | P1 | |||
IL18R1 | ENST00000409599.5 | c.302+1284C>T | intron_variant | 5 | P1 | ||||
IL18R1 | ENST00000410040.5 | c.302+1284C>T | intron_variant | 2 | |||||
IL18R1 | ENST00000677287.1 | c.302+1284C>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.218 AC: 33179AN: 151952Hom.: 4352 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.218 AC: 33187AN: 152070Hom.: 4354 Cov.: 33 AF XY: 0.218 AC XY: 16210AN XY: 74320
GnomAD4 genome
?
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33187
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152070
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33
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16210
AN XY:
74320
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1154
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3478
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
Score
Prediction
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