rs11465744
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_016584.3(IL23A):c.-35G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,358,458 control chromosomes in the GnomAD database, including 35 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 0.0083 ( 22 hom., cov: 31)
Exomes 𝑓: 0.00085 ( 13 hom. )
Consequence
IL23A
NM_016584.3 5_prime_UTR
NM_016584.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.639
Genes affected
IL23A (HGNC:15488): (interleukin 23 subunit alpha) This gene encodes a subunit of the heterodimeric cytokine interleukin 23 (IL23). IL23 is composed of this protein and the p40 subunit of interleukin 12 (IL12B). The receptor of IL23 is formed by the beta 1 subunit of IL12 (IL12RB1) and an IL23 specific subunit, IL23R. Both IL23 and IL12 can activate the transcription activator STAT4, and stimulate the production of interferon-gamma (IFNG). In contrast to IL12, which acts mainly on naive CD4(+) T cells, IL23 preferentially acts on memory CD4(+) T cells. [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=-0.86).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00835 (1271/152306) while in subpopulation AFR AF= 0.029 (1204/41556). AF 95% confidence interval is 0.0276. There are 22 homozygotes in gnomad4. There are 625 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 22 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL23A | NM_016584.3 | c.-35G>A | 5_prime_UTR_variant | 1/4 | ENST00000228534.6 | NP_057668.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL23A | ENST00000228534.6 | c.-35G>A | 5_prime_UTR_variant | 1/4 | 1 | NM_016584.3 | ENSP00000228534 | P1 | ||
IL23A | ENST00000619177.1 | n.108-416G>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
IL23A | ENST00000622119.4 | n.101-416G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00836 AC: 1273AN: 152188Hom.: 22 Cov.: 31
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GnomAD3 exomes AF: 0.00259 AC: 365AN: 140962Hom.: 8 AF XY: 0.00190 AC XY: 143AN XY: 75192
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GnomAD4 exome AF: 0.000846 AC: 1021AN: 1206152Hom.: 13 Cov.: 30 AF XY: 0.000800 AC XY: 465AN XY: 581032
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GnomAD4 genome AF: 0.00835 AC: 1271AN: 152306Hom.: 22 Cov.: 31 AF XY: 0.00839 AC XY: 625AN XY: 74464
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at