rs35449271
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000767.5(CYP2B6):c.1153-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00513 in 1,613,298 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000767.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2B6 | NM_000767.5 | c.1153-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000324071.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2B6 | ENST00000324071.10 | c.1153-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000767.5 | P1 | |||
CYP2B6 | ENST00000597612.1 | n.647+183C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
CYP2B6 | ENST00000593831.1 | c.445-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
CYP2B6 | ENST00000598834.2 | c.*593+183C>T | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00513 AC: 779AN: 151832Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00535 AC: 1344AN: 251230Hom.: 5 AF XY: 0.00554 AC XY: 752AN XY: 135792
GnomAD4 exome AF: 0.00513 AC: 7493AN: 1461350Hom.: 43 Cov.: 32 AF XY: 0.00508 AC XY: 3696AN XY: 726976
GnomAD4 genome AF: 0.00512 AC: 778AN: 151948Hom.: 5 Cov.: 32 AF XY: 0.00534 AC XY: 397AN XY: 74276
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | CYP2B6: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at