chr2-102384942-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_003855.5(IL18R1):c.753C>T(p.Phe251=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 1,600,312 control chromosomes in the GnomAD database, including 62,186 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 0.24 ( 4770 hom., cov: 32)
Exomes 𝑓: 0.28 ( 57416 hom. )
Consequence
IL18R1
NM_003855.5 synonymous
NM_003855.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.326
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP7
Synonymous conserved (PhyloP=0.326 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL18R1 | NM_003855.5 | c.753C>T | p.Phe251= | synonymous_variant | 7/11 | ENST00000233957.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL18R1 | ENST00000233957.7 | c.753C>T | p.Phe251= | synonymous_variant | 7/11 | 5 | NM_003855.5 | P1 | |
IL18R1 | ENST00000409599.5 | c.753C>T | p.Phe251= | synonymous_variant | 8/12 | 5 | P1 | ||
IL18R1 | ENST00000410040.5 | c.753C>T | p.Phe251= | synonymous_variant | 7/11 | 2 | |||
IL18R1 | ENST00000677287.1 | c.*297C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/11 |
Frequencies
GnomAD3 genomes AF: 0.239 AC: 36149AN: 151490Hom.: 4772 Cov.: 32
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GnomAD3 exomes AF: 0.258 AC: 64465AN: 250070Hom.: 8983 AF XY: 0.263 AC XY: 35551AN XY: 135222
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GnomAD4 exome AF: 0.277 AC: 401598AN: 1448702Hom.: 57416 Cov.: 30 AF XY: 0.278 AC XY: 200496AN XY: 721252
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GnomAD4 genome AF: 0.238 AC: 36158AN: 151610Hom.: 4770 Cov.: 32 AF XY: 0.238 AC XY: 17652AN XY: 74066
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at