22-42126753-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000106.6(CYP2D6):c.1316-1G>A variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as drug response (no stars).
Frequency
Consequence
NM_000106.6 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP2D6 | NM_000106.6 | c.1316-1G>A | splice_acceptor_variant, intron_variant | Intron 8 of 8 | ENST00000645361.2 | NP_000097.3 | ||
CYP2D6 | NM_001025161.3 | c.1163-1G>A | splice_acceptor_variant, intron_variant | Intron 7 of 7 | NP_001020332.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.15e-7 AC: 1AN: 1398892Hom.: 0 Cov.: 38 AF XY: 0.00 AC XY: 0AN XY: 690208
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
Tramadol response Other:1
- T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at