rs1362348
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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.302+96C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 1,340,974 control chromosomes in the GnomAD database, including 101,414 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 0.44 ( 16460 hom., cov: 33)
Exomes 𝑓: 0.37 ( 84954 hom. )
Consequence
IL18R1
NM_003855.5 intron
NM_003855.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.371
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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL18R1 | NM_003855.5 | c.302+96C>G | intron_variant | ENST00000233957.7 | NP_003846.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL18R1 | ENST00000233957.7 | c.302+96C>G | intron_variant | 5 | NM_003855.5 | ENSP00000233957 | P1 | |||
IL18R1 | ENST00000409599.5 | c.302+96C>G | intron_variant | 5 | ENSP00000387211 | P1 | ||||
IL18R1 | ENST00000410040.5 | c.302+96C>G | intron_variant | 2 | ENSP00000386663 | |||||
IL18R1 | ENST00000677287.1 | c.302+96C>G | intron_variant, NMD_transcript_variant | ENSP00000503023 |
Frequencies
GnomAD3 genomes AF: 0.439 AC: 66732AN: 152032Hom.: 16435 Cov.: 33
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GnomAD4 exome AF: 0.366 AC: 435685AN: 1188824Hom.: 84954 AF XY: 0.360 AC XY: 214585AN XY: 596248
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GnomAD4 genome AF: 0.439 AC: 66806AN: 152150Hom.: 16460 Cov.: 33 AF XY: 0.432 AC XY: 32170AN XY: 74382
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at