rs28399499
Variant summary
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 0.00364 in 1,614,058 control chromosomes in the GnomAD database, including 196 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 the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_000767.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0203 AC: 3085AN: 152082Hom.: 110 Cov.: 32
GnomAD3 exomes AF: 0.00508 AC: 1277AN: 251302Hom.: 54 AF XY: 0.00355 AC XY: 482AN XY: 135840
GnomAD4 exome AF: 0.00191 AC: 2791AN: 1461858Hom.: 85 Cov.: 32 AF XY: 0.00165 AC XY: 1202AN XY: 727236
GnomAD4 genome AF: 0.0203 AC: 3090AN: 152200Hom.: 111 Cov.: 32 AF XY: 0.0194 AC XY: 1447AN XY: 74420
ClinVar
Submissions by phenotype
CYP2B6-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
nevirapine response - Toxicity Other:1
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
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at