rs12721655
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000767.5(CYP2B6):c.415A>G(p.Lys139Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00384 in 1,614,004 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000767.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2B6 | NM_000767.5 | c.415A>G | p.Lys139Glu | missense_variant | 3/9 | ENST00000324071.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2B6 | ENST00000324071.10 | c.415A>G | p.Lys139Glu | missense_variant | 3/9 | 1 | NM_000767.5 | P1 | |
CYP2B6 | ENST00000593831.1 | c.187A>G | p.Lys63Glu | missense_variant | 2/5 | 2 | |||
CYP2B6 | ENST00000598834.2 | c.319A>G | p.Lys107Glu | missense_variant, NMD_transcript_variant | 3/10 | 5 | |||
CYP2B6 | ENST00000594187.1 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00251 AC: 381AN: 152058Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00233 AC: 585AN: 251312Hom.: 1 AF XY: 0.00221 AC XY: 300AN XY: 135832
GnomAD4 exome AF: 0.00398 AC: 5816AN: 1461828Hom.: 20 Cov.: 33 AF XY: 0.00379 AC XY: 2757AN XY: 727220
GnomAD4 genome ? AF: 0.00250 AC: 381AN: 152176Hom.: 2 Cov.: 31 AF XY: 0.00207 AC XY: 154AN XY: 74410
ClinVar
Submissions by phenotype
CYP2B6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 15, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at