chr2-102357669-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003855.5(IL18R1):c.-29+1269C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,770 control chromosomes in the GnomAD database, including 8,367 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign,association (★★).
Frequency
Genomes: 𝑓 0.32 ( 8367 hom., cov: 30)
Consequence
IL18R1
NM_003855.5 intron
NM_003855.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.25
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 2-102357669-C-T is Benign according to our data. Variant chr2-102357669-C-T is described in ClinVar as [Benign, association]. Clinvar id is 916546.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL18R1 | ENST00000233957.7 | c.-29+1269C>T | intron_variant | 5 | NM_003855.5 | ENSP00000233957.1 | ||||
IL18R1 | ENST00000409599.5 | c.-29+1269C>T | intron_variant | 5 | ENSP00000387211.1 | |||||
IL18R1 | ENST00000410040.5 | c.-28-4964C>T | intron_variant | 2 | ENSP00000386663.1 | |||||
IL18R1 | ENST00000466357.1 | n.356+1269C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.316 AC: 47973AN: 151652Hom.: 8366 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.316 AC: 47996AN: 151770Hom.: 8367 Cov.: 30 AF XY: 0.317 AC XY: 23503AN XY: 74154
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ClinVar
Significance: Benign; association
Submissions summary: Benign:1Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 13, 2018 | This variant is associated with the following publications: (PMID: 28121058) - |
Behcet disease Other:1
association, criteria provided, single submitter | case-control | Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, The First Affiliated Hospital of Chongqing Medical University | Jan 29, 2020 | - - |
Computational 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