rs2045387
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000600835.6(IL12RB1):c.-109-2844C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,260 control chromosomes in the GnomAD database, including 3,249 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 0.18 ( 3249 hom., cov: 33)
Consequence
IL12RB1
ENST00000600835.6 intron
ENST00000600835.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0180
Genes affected
IL12RB1 (HGNC:5971): (interleukin 12 receptor subunit beta 1) The protein encoded by this gene is a type I transmembrane protein that belongs to the hemopoietin receptor superfamily. This protein binds to interleukine 12 (IL12) with a low affinity, and is thought to be a part of IL12 receptor complex. This protein forms a disulfide-linked oligomer, which is required for its IL12 binding activity. The coexpression of this and IL12RB2 proteins was shown to lead to the formation of high-affinity IL12 binding sites and reconstitution of IL12 dependent signaling. Mutations in this gene impair the development of interleukin-17-producing T lymphocytes and result in increased susceptibility to mycobacterial and Salmonella infections. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
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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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL12RB1 | NM_001290024.1 | c.12-2844C>A | intron_variant | NP_001276953.1 | ||||
IL12RB1 | XM_006722741.4 | c.12-2844C>A | intron_variant | XP_006722804.2 | ||||
IL12RB1 | XM_011527966.3 | c.12-2844C>A | intron_variant | XP_011526268.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL12RB1 | ENST00000600835.6 | c.-109-2844C>A | intron_variant | 1 | ENSP00000470788 | P1 | ||||
IL12RB1 | ENST00000594176.1 | c.-110+874C>A | intron_variant | 4 | ENSP00000473051 | |||||
IL12RB1 | ENST00000598019.6 | c.-110+874C>A | intron_variant | 4 | ENSP00000468831 |
Frequencies
GnomAD3 genomes AF: 0.182 AC: 27708AN: 152142Hom.: 3254 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.182 AC: 27694AN: 152260Hom.: 3249 Cov.: 33 AF XY: 0.183 AC XY: 13603AN XY: 74454
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at