rs2279343
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000767.5(CYP2B6):c.785A>G(p.Lys262Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2B6 | ENST00000324071.10 | c.785A>G | p.Lys262Arg | missense_variant | Exon 5 of 9 | 1 | NM_000767.5 | ENSP00000324648.2 | ||
CYP2B6 | ENST00000593831.1 | c.257-2940A>G | intron_variant | Intron 2 of 4 | 2 | ENSP00000470582.1 | ||||
CYP2B6 | ENST00000598834.2 | n.*226A>G | non_coding_transcript_exon_variant | Exon 6 of 10 | 5 | ENSP00000496294.1 | ||||
CYP2B6 | ENST00000598834.2 | n.*226A>G | 3_prime_UTR_variant | Exon 6 of 10 | 5 | ENSP00000496294.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 42549AN: 145088Hom.: 6480 Cov.: 25 FAILED QC
GnomAD3 exomes AF: 0.129 AC: 27016AN: 208848Hom.: 7469 AF XY: 0.129 AC XY: 14529AN XY: 112738
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.164 AC: 187493AN: 1142912Hom.: 38948 Cov.: 36 AF XY: 0.173 AC XY: 98990AN XY: 573654
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.293 AC: 42562AN: 145210Hom.: 6478 Cov.: 25 AF XY: 0.293 AC XY: 20728AN XY: 70634
ClinVar
Submissions by phenotype
Efavirenz response Benign:2Other:1
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not provided Benign:1
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CYP2B6-related disorder Benign:1
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