rs3181842
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000767.5(CYP2B6):c.*284C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 212,720 control chromosomes in the GnomAD database, including 47,826 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 0.66 ( 33508 hom., cov: 30)
Exomes 𝑓: 0.68 ( 14318 hom. )
Consequence
CYP2B6
NM_000767.5 3_prime_UTR
NM_000767.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.71
Genes affected
CYP2B6 (HGNC:2615): (cytochrome P450 family 2 subfamily B member 6) This gene, CYP2B6, encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and its expression is induced by phenobarbital. The enzyme is known to metabolize some xenobiotics, such as the anti-cancer drugs cyclophosphamide and ifosphamide. Transcript variants for this gene have been described; however, it has not been resolved whether these transcripts are in fact produced by this gene or by a closely related pseudogene, CYP2B7. Both the gene and the pseudogene are located in the middle of a CYP2A pseudogene found in a large cluster of cytochrome P450 genes from the CYP2A, CYP2B and CYP2F subfamilies on chromosome 19q. [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=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2B6 | NM_000767.5 | c.*284C>T | 3_prime_UTR_variant | 9/9 | ENST00000324071.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2B6 | ENST00000324071.10 | c.*284C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_000767.5 | P1 | ||
CYP2B6 | ENST00000597612.1 | n.1113C>T | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
CYP2B6 | ENST00000593831.1 | c.*284C>T | 3_prime_UTR_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.661 AC: 100239AN: 151642Hom.: 33465 Cov.: 30
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GnomAD4 exome AF: 0.681 AC: 41533AN: 60962Hom.: 14318 Cov.: 2 AF XY: 0.691 AC XY: 21922AN XY: 31718
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GnomAD4 genome ? AF: 0.661 AC: 100335AN: 151758Hom.: 33508 Cov.: 30 AF XY: 0.668 AC XY: 49527AN XY: 74172
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at