Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000767.5(CYP2B6):c.983T>C(p.Ile328Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 152082 control chromosomes in the gnomAD Genomes database, including 110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Verdict is Benign. Variant got -12 ACMG points.
|CYP2B6||ENST00000598834.2 ||c.*424T>C||3_prime_UTR_variant, NMD_transcript_variant||8/10||5|
GnomAD3 genomes AF: 0.0203AC: 3085AN: 152082Hom.: 110Cov.: 32 GnomAD3 exomes AF: 0.00508AC: 1277AN: 251302Hom.: 54 AF XY: 0.00355AC XY: 482AN XY: 135840 GnomAD4 exome AF: 0.00191AC: 2791AN: 1461858Hom.: 85 AF XY: 0.00165AC XY: 1202AN XY: 727236
Submissions by phenotype
nevirapine response - Toxicity
|drug response, reviewed by expert panel||curation||PharmGKB||Mar 24, 2021||PharmGKB Level of Evidence 2A: Variants in Level 2A clinical annotations are found in PharmGKB’s Tier 1 Very Important Pharmacogenes (VIPs). These variants are in known pharmacogenes, implying causation of drug phenotype is more likely. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2A clinical annotations must be supported by at least two independent publications. Drug-variant association: Toxicity|
Find out detailed SpliceAI scores and Pangolin per-transcript scores at