rs10889677
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_144701(IL23R):c.*309C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151888 control chromosomes in the gnomAD Genomes database, including 7310 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 0.28 ( 7310 hom., cov: 32)
Consequence
IL23R
NM_144701 3_prime_UTR
NM_144701 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.209
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL23R | NM_144701.3 | c.*309C>A | 3_prime_UTR_variant | 11/11 | ENST00000347310.10 | ||
IL23R | XM_011540790.4 | c.*309C>A | 3_prime_UTR_variant | 11/11 | |||
IL23R | XM_011540791.4 | c.*309C>A | 3_prime_UTR_variant | 11/11 | |||
IL23R | XM_047447227.1 | c.1239+3510C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL23R | ENST00000347310.10 | c.*309C>A | 3_prime_UTR_variant | 11/11 | 1 | NM_144701.3 | P1 | ||
IL23R | ENST00000473881.2 | c.*1025C>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.285 AC: 43213AN: 151888Hom.: 7310 Cov.: 32
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GnomAD4 exome AF: 0.355 AC: 74117AN: 208754Hom.: 15257 AF XY: 0.373 AC XY: 41629AN XY: 111556
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at