19-41012465-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000767.5(CYP2B6):c.1132C>T(p.Arg378Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as drug response (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000767.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2B6 | NM_000767.5 | c.1132C>T | p.Arg378Ter | stop_gained | 7/9 | ENST00000324071.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2B6 | ENST00000324071.10 | c.1132C>T | p.Arg378Ter | stop_gained | 7/9 | 1 | NM_000767.5 | P1 | |
CYP2B6 | ENST00000597612.1 | n.627C>T | non_coding_transcript_exon_variant | 2/3 | 1 | ||||
CYP2B6 | ENST00000593831.1 | c.424C>T | p.Arg142Ter | stop_gained | 3/5 | 2 | |||
CYP2B6 | ENST00000598834.2 | c.*573C>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251234Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135766
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.0000358 AC XY: 26AN XY: 727234
GnomAD4 genome AF: 0.000125 AC: 19AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74316
ClinVar
Submissions by phenotype
Efavirenz response Other:1
drug response, no assertion criteria provided | research | Institute of Microbiology; University Hospital and Univeristy of Lausanne | Jan 01, 2006 | - This variant was associated with very high efavirenz plasma levels in a HIV+individual |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at