chr22-42129180-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000106.6(CYP2D6):c.358T>A(p.Phe120Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000499 in 1,604,188 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F120L) has been classified as Uncertain significance.
Frequency
Consequence
NM_000106.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2D6 | NM_000106.6 | c.358T>A | p.Phe120Ile | missense_variant | 3/9 | ENST00000645361.2 | |
CYP2D6 | NM_001025161.3 | c.353-236T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2D6 | ENST00000645361.2 | c.358T>A | p.Phe120Ile | missense_variant | 3/9 | NM_000106.6 | P1 | ||
NDUFA6-DT | ENST00000439129.5 | n.1718+3773A>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000502 AC: 76AN: 151398Hom.: 7 Cov.: 33
GnomAD3 exomes AF: 0.00165 AC: 396AN: 239358Hom.: 12 AF XY: 0.00155 AC XY: 203AN XY: 131082
GnomAD4 exome AF: 0.000499 AC: 725AN: 1452678Hom.: 23 Cov.: 37 AF XY: 0.000487 AC XY: 352AN XY: 722984
GnomAD4 genome AF: 0.000502 AC: 76AN: 151510Hom.: 7 Cov.: 33 AF XY: 0.000567 AC XY: 42AN XY: 74072
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at