rs3745274
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM2_SupportingBP4_StrongBP7
The NM_000767(CYP2B6):c.516G>A(p.Gln172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000040 ( 0 hom. )
Consequence
CYP2B6
NM_000767 synonymous
NM_000767 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.968
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 31.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP7
?
Synonymous conserved (PhyloP=-0.968 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2B6 | NM_000767.5 | c.516G>A | p.Gln172= | synonymous_variant | 4/9 | ENST00000324071.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2B6 | ENST00000324071.10 | c.516G>A | p.Gln172= | synonymous_variant | 4/9 | 1 | NM_000767.5 | P1 | |
CYP2B6 | ENST00000593831.1 | c.256+2490G>A | intron_variant | 2 | |||||
CYP2B6 | ENST00000594187.1 | n.100G>A | non_coding_transcript_exon_variant | 2/2 | 5 | ||||
CYP2B6 | ENST00000598834.2 | c.420G>A | p.Gln140= | synonymous_variant, NMD_transcript_variant | 4/10 | 5 |
Frequencies
GnomAD3 genomesCov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251268Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135780
GnomAD3 exomes
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461768Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 727172
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at