chr1-67313993-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001374259.2(IL12RB2):c.-44A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,084 control chromosomes in the GnomAD database, including 14,883 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 0.42 ( 14883 hom., cov: 32)
Exomes 𝑓: 0.17 ( 0 hom. )
Consequence
IL12RB2
NM_001374259.2 5_prime_UTR
NM_001374259.2 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.840
Genes affected
IL12RB2 (HGNC:5972): (interleukin 12 receptor subunit beta 2) The protein encoded by this gene is a type I transmembrane protein identified as a subunit of the interleukin 12 receptor complex. The coexpression of this and IL12RB1 proteins was shown to lead to the formation of high-affinity IL12 binding sites and reconstitution of IL12 dependent signaling. The expression of this gene is up-regulated by interferon gamma in Th1 cells, and plays a role in Th1 cell differentiation. The up-regulation of this gene is found to be associated with a number of infectious diseases, such as Crohn's disease and leprosy, which is thought to contribute to the inflammatory response and host defense. Several transcript variants encoding different isoforms and non-protein coding transcripts have been found for this gene. [provided by RefSeq, Apr 2012]
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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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL12RB2 | NM_001374259.2 | c.-44A>G | 5_prime_UTR_variant | 2/17 | ENST00000674203.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL12RB2 | ENST00000674203.2 | c.-44A>G | 5_prime_UTR_variant | 2/17 | NM_001374259.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.418 AC: 63515AN: 151960Hom.: 14843 Cov.: 32
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GnomAD4 exome AF: 0.167 AC: 1AN: 6Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 4
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GnomAD4 genome AF: 0.418 AC: 63610AN: 152078Hom.: 14883 Cov.: 32 AF XY: 0.412 AC XY: 30626AN XY: 74354
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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