rs10889657
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000637002.1(IL23R):c.-30+10643T>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,986 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Consequence
ENST00000637002.1 intron, NMD_transcript
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL23R | XM_011540790.4 | c.-30+10643T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL23R | ENST00000637002.1 | c.-30+10643T>A | intron_variant, NMD_transcript_variant | 1 | |||||
C1orf141 | ENST00000371007.6 | c.-103-18577A>T | intron_variant | 5 | P1 | ||||
C1orf141 | ENST00000448166.6 | c.-103-18577A>T | intron_variant | 5 | |||||
IL23R | ENST00000697222.1 | c.-30+10643T>A | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151986Hom.: 0 Cov.: 32
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151986Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74224
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at