rs1343151
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_144701.3(IL23R):c.1149-2391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,018 control chromosomes in the GnomAD database, including 15,100 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 0.40 ( 15100 hom., cov: 32)
Consequence
IL23R
NM_144701.3 intron
NM_144701.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0970
Genes affected
IL23R (HGNC:19100): (interleukin 23 receptor) The protein encoded by this gene is a subunit of the receptor for IL23A/IL23. This protein pairs with the receptor molecule IL12RB1/IL12Rbeta1, and both are required for IL23A signaling. This protein associates constitutively with Janus kinase 2 (JAK2), and also binds to transcription activator STAT3 in a ligand-dependent manner. [provided by RefSeq, Jul 2008]
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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 = 0.674 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL23R | NM_144701.3 | c.1149-2391G>A | intron_variant | ENST00000347310.10 | NP_653302.2 | |||
IL23R | XM_011540790.4 | c.1149-2391G>A | intron_variant | XP_011539092.1 | ||||
IL23R | XM_011540791.4 | c.1149-2391G>A | intron_variant | XP_011539093.1 | ||||
IL23R | XM_047447227.1 | c.1149-2391G>A | intron_variant | XP_047303183.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL23R | ENST00000347310.10 | c.1149-2391G>A | intron_variant | 1 | NM_144701.3 | ENSP00000321345 | P1 |
Frequencies
GnomAD3 genomes AF: 0.404 AC: 61345AN: 151900Hom.: 15079 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.404 AC: 61408AN: 152018Hom.: 15100 Cov.: 32 AF XY: 0.390 AC XY: 28946AN XY: 74310
GnomAD4 genome
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625
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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