rs2516564
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000258807.5(CIDEB):c.-414-607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,200 control chromosomes in the GnomAD database, including 2,932 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 ( 2932 hom., cov: 32)
Exomes 𝑓: 0.15 ( 0 hom. )
Consequence
CIDEB
ENST00000258807.5 intron
ENST00000258807.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.657
Genes affected
CIDEB (HGNC:1977): (cell death inducing DFFA like effector b) Enables identical protein binding activity. Involved in activation of cysteine-type endopeptidase activity; positive regulation of cell death; and positive regulation of release of cytochrome c from mitochondria. Acts upstream of or within apoptotic process. Located in cytosol and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
LTB4R2 (HGNC:19260): (leukotriene B4 receptor 2) Predicted to enable G protein-coupled peptide receptor activity and leukotriene B4 receptor activity. Predicted to be involved in inflammatory response and neuropeptide signaling pathway. Predicted to act upstream of or within keratinocyte migration and signal transduction. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIDEB | NM_001393334.1 | c.-1021G>A | 5_prime_UTR_variant | 2/7 | |||
CIDEB | NM_001318807.3 | c.-414-607G>A | intron_variant | ||||
CIDEB | NM_001393335.1 | c.-447-607G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIDEB | ENST00000258807.5 | c.-414-607G>A | intron_variant | 1 | P1 | ||||
LTB4R2 | ENST00000528054.1 | c.-1135C>T | 5_prime_UTR_variant | 1/1 | |||||
CIDEB | ENST00000336557.9 | c.-414-607G>A | intron_variant | 2 | P1 | ||||
LTB4R2 | ENST00000527924.6 | c.-95-734C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.184 AC: 27967AN: 152028Hom.: 2931 Cov.: 32
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GnomAD4 exome AF: 0.148 AC: 8AN: 54Hom.: 0 Cov.: 0 AF XY: 0.156 AC XY: 5AN XY: 32
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GnomAD4 genome ? AF: 0.184 AC: 27980AN: 152146Hom.: 2932 Cov.: 32 AF XY: 0.179 AC XY: 13276AN XY: 74374
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at