chr2-102418659-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003853.4(IL18RAP):c.-619T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,116 control chromosomes in the GnomAD database, including 23,638 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 0.54 ( 23630 hom., cov: 32)
Exomes 𝑓: 0.48 ( 8 hom. )
Consequence
IL18RAP
NM_003853.4 5_prime_UTR
NM_003853.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.54
Genes affected
IL18RAP (HGNC:5989): (interleukin 18 receptor accessory protein) The protein encoded by this gene is an accessory subunit of the heterodimeric receptor for interleukin 18 (IL18), a proinflammatory cytokine involved in inducing cell-mediated immunity. This protein enhances the IL18-binding activity of the IL18 receptor and plays a role in signaling by IL18. Mutations in this gene are associated with Crohn's disease and inflammatory bowel disease, and susceptibility to celiac disease and leprosy. Alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Feb 2014]
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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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL18RAP | NM_001393488.1 | c.-1249T>C | 5_prime_UTR_variant | 1/12 | |||
IL18RAP | NM_003853.4 | c.-619T>C | 5_prime_UTR_variant | 1/12 | |||
IL18RAP | NM_001393486.1 | c.-489+10T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL18RAP | ENST00000264260.6 | upstream_gene_variant | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.535 AC: 81283AN: 151916Hom.: 23599 Cov.: 32
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GnomAD4 exome AF: 0.476 AC: 40AN: 84Hom.: 8 Cov.: 0 AF XY: 0.500 AC XY: 22AN XY: 44
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GnomAD4 genome AF: 0.535 AC: 81366AN: 152032Hom.: 23630 Cov.: 32 AF XY: 0.529 AC XY: 39290AN XY: 74278
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at