chr19-40991367-A-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_000767.5(CYP2B6):c.62A>T(p.Gln21Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00521 in 1,614,030 control chromosomes in the GnomAD database, including 31 homozygotes. 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 Likely benign (no stars). 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP2B6 | NM_000767.5 | c.62A>T | p.Gln21Leu | missense_variant | 1/9 | ENST00000324071.10 | NP_000758.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2B6 | ENST00000324071.10 | c.62A>T | p.Gln21Leu | missense_variant | 1/9 | 1 | NM_000767.5 | ENSP00000324648 | P1 | |
CYP2B6 | ENST00000598834.2 | upstream_gene_variant | 5 | ENSP00000496294 |
Frequencies
GnomAD3 genomes AF: 0.00422 AC: 641AN: 152050Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00418 AC: 1052AN: 251442Hom.: 4 AF XY: 0.00432 AC XY: 587AN XY: 135896
GnomAD4 exome AF: 0.00532 AC: 7775AN: 1461864Hom.: 28 Cov.: 31 AF XY: 0.00523 AC XY: 3805AN XY: 727232
GnomAD4 genome AF: 0.00421 AC: 641AN: 152166Hom.: 3 Cov.: 31 AF XY: 0.00390 AC XY: 290AN XY: 74388
ClinVar
Submissions by phenotype
CYP2B6-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 09, 2019 | 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