NM_000106.6:c.1315+32T>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000106.6(CYP2D6):c.1315+32T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000664 in 150,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 30)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CYP2D6
NM_000106.6 intron
NM_000106.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.473
Publications
0 publications found
Genes affected
CYP2D6 (HGNC:2625): (cytochrome P450 family 2 subfamily D member 6) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and is known to metabolize as many as 25% of commonly prescribed drugs. Its substrates include antidepressants, antipsychotics, analgesics and antitussives, beta adrenergic blocking agents, antiarrythmics and antiemetics. The gene is highly polymorphic in the human population; certain alleles result in the poor metabolizer phenotype, characterized by a decreased ability to metabolize the enzyme's substrates. Some individuals with the poor metabolizer phenotype have no functional protein since they carry 2 null alleles whereas in other individuals the gene is absent. This gene can vary in copy number and individuals with the ultrarapid metabolizer phenotype can have 3 or more active copies of the gene. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000106.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CYP2D6 | NM_000106.6 | MANE Select | c.1315+32T>A | intron | N/A | NP_000097.3 | |||
| CYP2D6 | NM_001025161.3 | c.1162+32T>A | intron | N/A | NP_001020332.2 | P10635-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CYP2D6 | ENST00000645361.2 | MANE Select | c.1315+32T>A | intron | N/A | ENSP00000496150.1 | P10635-1 | ||
| CYP2D6 | ENST00000359033.4 | TSL:1 | c.1162+32T>A | intron | N/A | ENSP00000351927.4 | P10635-2 | ||
| CYP2D6 | ENST00000360124.10 | TSL:1 | n.*390+32T>A | intron | N/A | ENSP00000353241.6 | H7BY38 |
Frequencies
GnomAD3 genomes 0.00000665 AC: 1AN: 150422Hom.: 0 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
150422
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.16e-7 AC: 1AN: 1396680Hom.: 0 Cov.: 38 AF XY: 0.00000145 AC XY: 1AN XY: 689026 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
1396680
Hom.:
Cov.:
38
AF XY:
AC XY:
1
AN XY:
689026
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31498
American (AMR)
AF:
AC:
0
AN:
35712
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25182
East Asian (EAS)
AF:
AC:
0
AN:
36050
South Asian (SAS)
AF:
AC:
1
AN:
79116
European-Finnish (FIN)
AF:
AC:
0
AN:
49330
Middle Eastern (MID)
AF:
AC:
0
AN:
4916
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1077070
Other (OTH)
AF:
AC:
0
AN:
57806
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000664 AC: 1AN: 150534Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 73508 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
150534
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
73508
show subpopulations
African (AFR)
AF:
AC:
0
AN:
40720
American (AMR)
AF:
AC:
0
AN:
15140
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5104
South Asian (SAS)
AF:
AC:
1
AN:
4744
European-Finnish (FIN)
AF:
AC:
0
AN:
10570
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67520
Other (OTH)
AF:
AC:
0
AN:
2072
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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