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GeneBe

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

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
CYP2D6NM_000106.6 linkuse as main transcriptc.506-1G>T splice_acceptor_variant ENST00000645361.2
CYP2D6NM_001025161.3 linkuse as main transcriptc.353-1G>T splice_acceptor_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP2D6ENST00000645361.2 linkuse as main transcriptc.506-1G>T splice_acceptor_variant NM_000106.6 P1P10635-1
NDUFA6-DTENST00000439129.5 linkuse as main transcriptn.1718+3538C>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.15
D
BayesDel_noAF
Uncertain
-0.030
Cadd
Pathogenic
33
Dann
Uncertain
0.98
Eigen
Pathogenic
0.76
Eigen_PC
Uncertain
0.50
FATHMM_MKL
Pathogenic
0.98
D
MutationTaster
Benign
1.0
D;D;D
GERP RS
3.4

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.94
DS_AG_spliceai
0.90
Position offset: -37
DS_AL_spliceai
1.0
Position offset: -1
DS_DG_spliceai
0.0
Position offset: -30
DS_DL_spliceai
0.0
Position offset: -38

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-42524947;