rs1008193
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_144701.3(IL23R):c.1149-1609C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,842 control chromosomes in the GnomAD database, including 3,707 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 0.21 ( 3707 hom., cov: 31)
Consequence
IL23R
NM_144701.3 intron
NM_144701.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.283
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=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL23R | NM_144701.3 | c.1149-1609C>G | intron_variant | ENST00000347310.10 | |||
IL23R | XM_011540790.4 | c.1149-1609C>G | intron_variant | ||||
IL23R | XM_011540791.4 | c.1149-1609C>G | intron_variant | ||||
IL23R | XM_047447227.1 | c.1149-1609C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL23R | ENST00000347310.10 | c.1149-1609C>G | intron_variant | 1 | NM_144701.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.209 AC: 31728AN: 151722Hom.: 3706 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.209 AC: 31740AN: 151842Hom.: 3707 Cov.: 31 AF XY: 0.201 AC XY: 14897AN XY: 74222
GnomAD4 genome
?
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31740
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151842
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31
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14897
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74222
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494
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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