rs3213732
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003855.5(IL18R1):c.688+137A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 654,156 control chromosomes in the GnomAD database, including 79,439 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 0.53 ( 23532 hom., cov: 31)
Exomes 𝑓: 0.45 ( 55907 hom. )
Consequence
IL18R1
NM_003855.5 intron
NM_003855.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.592
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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL18R1 | NM_003855.5 | c.688+137A>G | intron_variant | ENST00000233957.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL18R1 | ENST00000233957.7 | c.688+137A>G | intron_variant | 5 | NM_003855.5 | P1 | |||
IL18R1 | ENST00000409599.5 | c.688+137A>G | intron_variant | 5 | P1 | ||||
IL18R1 | ENST00000410040.5 | c.688+137A>G | intron_variant | 2 | |||||
IL18R1 | ENST00000677287.1 | c.*232+137A>G | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.534 AC: 81084AN: 151840Hom.: 23500 Cov.: 31
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GnomAD4 exome AF: 0.455 AC: 228265AN: 502198Hom.: 55907 AF XY: 0.443 AC XY: 117817AN XY: 265772
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GnomAD4 genome ? AF: 0.534 AC: 81169AN: 151958Hom.: 23532 Cov.: 31 AF XY: 0.528 AC XY: 39205AN XY: 74272
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ClinVar
Not reported inComputational scores
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Name
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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