1-67165650-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000637002.1(IL23R):c.-29-2442C>T variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,102 control chromosomes in the GnomAD database, including 17,719 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 0.47 ( 17719 hom., cov: 33)
Consequence
IL23R
ENST00000637002.1 intron, NMD_transcript
ENST00000637002.1 intron, NMD_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.26
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL23R | XM_011540790.4 | c.-29-2442C>T | intron_variant | ||||
IL23R | XM_011540791.4 | c.-29-2442C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL23R | ENST00000637002.1 | c.-29-2442C>T | intron_variant, NMD_transcript_variant | 1 | |||||
C1orf141 | ENST00000371007.6 | c.-103-34423G>A | intron_variant | 5 | P1 | ||||
C1orf141 | ENST00000448166.6 | c.-103-34423G>A | intron_variant | 5 | |||||
IL23R | ENST00000697222.1 | c.-29-2442C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.471 AC: 71641AN: 151984Hom.: 17718 Cov.: 33
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.471 AC: 71648AN: 152102Hom.: 17719 Cov.: 33 AF XY: 0.472 AC XY: 35083AN XY: 74350
GnomAD4 genome
?
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1913
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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