rs3892097
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting
The NM_000106(CYP2D6):c.506-1G>T variant causes a splice acceptor change. The variant was absent in control chromosomes in GnomAD Genomes project. 2/2 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
CYP2D6
NM_000106 splice_acceptor
NM_000106 splice_acceptor
Scores
2
4
1
Splicing: ADA: 1.000
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.88
Links
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2D6 | NM_000106.6 | c.506-1G>T | splice_acceptor_variant | ENST00000645361.2 | |||
CYP2D6 | NM_001025161.3 | c.353-1G>T | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2D6 | ENST00000645361.2 | c.506-1G>T | splice_acceptor_variant | NM_000106.6 | P1 | ||||
NDUFA6-DT | ENST00000439129.5 | n.1718+3538C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomesCov.: 32
GnomAD3 genomes
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
D;D;D
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
DS_AG_spliceai
Position offset: -37
DS_AL_spliceai
Position offset: -1
DS_DG_spliceai
Position offset: -30
DS_DL_spliceai
Position offset: -38
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.