rs11574790
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002187.3(IL12B):c.856-22C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,612,714 control chromosomes in the GnomAD database, including 11,178 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 1471 hom., cov: 33)
Exomes 𝑓: 0.11 ( 9707 hom. )
Consequence
IL12B
NM_002187.3 intron
NM_002187.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.292
Genes affected
IL12B (HGNC:5970): (interleukin 12B) This gene encodes a subunit of interleukin 12, a cytokine that acts on T and natural killer cells, and has a broad array of biological activities. Interleukin 12 is a disulfide-linked heterodimer composed of the 40 kD cytokine receptor like subunit encoded by this gene, and a 35 kD subunit encoded by IL12A. This cytokine is expressed by activated macrophages that serve as an essential inducer of Th1 cells development. This cytokine has been found to be important for sustaining a sufficient number of memory/effector Th1 cells to mediate long-term protection to an intracellular pathogen. Overexpression of this gene was observed in the central nervous system of patients with multiple sclerosis (MS), suggesting a role of this cytokine in the pathogenesis of the disease. The promoter polymorphism of this gene has been reported to be associated with the severity of atopic and non-atopic asthma in children. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 5-159316838-G-A is Benign according to our data. Variant chr5-159316838-G-A is described in ClinVar as [Benign]. Clinvar id is 2628273.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL12B | NM_002187.3 | c.856-22C>T | intron_variant | ENST00000231228.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL12B | ENST00000231228.3 | c.856-22C>T | intron_variant | 1 | NM_002187.3 | P1 | |||
IL12B | ENST00000696750.1 | c.226-22C>T | intron_variant | ||||||
IL12B | ENST00000696751.1 | c.*351-22C>T | intron_variant, NMD_transcript_variant | ||||||
ENST00000521472.6 | n.289+5424G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.132 AC: 20124AN: 152132Hom.: 1464 Cov.: 33
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GnomAD3 exomes AF: 0.116 AC: 28627AN: 245750Hom.: 2026 AF XY: 0.111 AC XY: 14835AN XY: 133172
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GnomAD4 exome AF: 0.110 AC: 161074AN: 1460464Hom.: 9707 Cov.: 32 AF XY: 0.109 AC XY: 78930AN XY: 726546
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GnomAD4 genome ? AF: 0.132 AC: 20148AN: 152250Hom.: 1471 Cov.: 33 AF XY: 0.128 AC XY: 9519AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 24% of patients studied by a panel of primary immunodeficiencies. Number of patients: 23. Only high quality variants are reported. - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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