rs5030865
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000106.6(CYP2D6):c.505G>T(p.Gly169Ter) variant causes a stop gained, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000349 in 1,606,104 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign,other (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000106.6 stop_gained, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2D6 | NM_000106.6 | c.505G>T | p.Gly169Ter | stop_gained, splice_region_variant | 3/9 | ENST00000645361.2 | |
CYP2D6 | NM_001025161.3 | c.353-89G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2D6 | ENST00000645361.2 | c.505G>T | p.Gly169Ter | stop_gained, splice_region_variant | 3/9 | NM_000106.6 | P1 | ||
NDUFA6-DT | ENST00000439129.5 | n.1718+3626C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151464Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000669 AC: 16AN: 239014Hom.: 0 AF XY: 0.0000999 AC XY: 13AN XY: 130128
GnomAD4 exome AF: 0.0000357 AC: 52AN: 1454640Hom.: 1 Cov.: 76 AF XY: 0.0000442 AC XY: 32AN XY: 723178
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151464Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 73946
ClinVar
Submissions by phenotype
not provided Benign:1Other:1
other, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 06, 2018 | - Variant classified as "other reportable" ??? variant is clinically benign (not associated with disease) but is reported when observed (e.g. pseudodeficiency alleles). |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Debrisoquine, poor metabolism of Other:1
drug response, no assertion criteria provided | literature only | OMIM | Nov 01, 1995 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at