chr22-42130667-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM5BP4_StrongBS2
The NM_000106.6(CYP2D6):c.125G>A(p.Gly42Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000945 in 1,608,898 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G42R) has been classified as Likely benign.
Frequency
Consequence
NM_000106.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2D6 | NM_000106.6 | c.125G>A | p.Gly42Glu | missense_variant | 1/9 | ENST00000645361.2 | |
CYP2D6 | NM_001025161.3 | c.125G>A | p.Gly42Glu | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2D6 | ENST00000645361.2 | c.125G>A | p.Gly42Glu | missense_variant | 1/9 | NM_000106.6 | P1 | ||
NDUFA6-DT | ENST00000439129.5 | n.1718+5260C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000212 AC: 32AN: 150728Hom.: 1 Cov.: 30
GnomAD3 exomes AF: 0.000239 AC: 59AN: 246470Hom.: 2 AF XY: 0.000240 AC XY: 32AN XY: 133508
GnomAD4 exome AF: 0.0000816 AC: 119AN: 1458058Hom.: 4 Cov.: 32 AF XY: 0.0000841 AC XY: 61AN XY: 725158
GnomAD4 genome AF: 0.000219 AC: 33AN: 150840Hom.: 1 Cov.: 30 AF XY: 0.0000949 AC XY: 7AN XY: 73732
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at