chr22-42126667-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_000106.6(CYP2D6):c.1401G>A(p.Ser467=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000367 in 1,606,208 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars). Synonymous variant affecting the same amino acid position (i.e. S467S) has been classified as Benign.
Frequency
Consequence
NM_000106.6 synonymous
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 | UniProt |
---|---|---|---|---|---|---|---|
CYP2D6 | NM_000106.6 | c.1401G>A | p.Ser467= | synonymous_variant | 9/9 | ENST00000645361.2 | |
CYP2D6 | NM_001025161.3 | c.1248G>A | p.Ser416= | synonymous_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2D6 | ENST00000645361.2 | c.1401G>A | p.Ser467= | synonymous_variant | 9/9 | NM_000106.6 | P1 | ||
NDUFA6-DT | ENST00000439129.5 | n.1718+1260C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000667 AC: 1AN: 149992Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000206 AC: 5AN: 242510Hom.: 0 AF XY: 0.0000305 AC XY: 4AN XY: 131278
GnomAD4 exome AF: 0.0000398 AC: 58AN: 1456216Hom.: 1 Cov.: 38 AF XY: 0.0000470 AC XY: 34AN XY: 723984
GnomAD4 genome AF: 0.00000667 AC: 1AN: 149992Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73224
ClinVar
Submissions by phenotype
Tramadol response Other:1
drug response, no assertion criteria provided | research | Bruce Budowle Laboratory, University of North Texas Health Science Center | Apr 28, 2018 | - 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