22-42130571-G-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_000106.6(CYP2D6):c.180+41C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 924,438 control chromosomes in the GnomAD database, including 24,431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.047 ( 378 hom., cov: 23)
Exomes 𝑓: 0.080 ( 24431 hom. )
Failed GnomAD Quality Control
Consequence
CYP2D6
NM_000106.6 intron
NM_000106.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.66
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 made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (Cadd=0.132).
BP6
Variant 22-42130571-G-T is Benign according to our data. Variant chr22-42130571-G-T is described in Lovd as [Benign].
BA1
GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2D6 | ENST00000645361.2 | c.180+41C>A | intron_variant | Intron 1 of 8 | NM_000106.6 | ENSP00000496150.1 | ||||
CYP2D6 | ENST00000359033.4 | c.180+41C>A | intron_variant | Intron 1 of 7 | 1 | ENSP00000351927.4 | ||||
CYP2D6 | ENST00000488442.1 | n.243C>A | non_coding_transcript_exon_variant | Exon 1 of 8 | 5 | |||||
NDUFA6-DT | ENST00000439129.5 | n.1718+5164G>T | intron_variant | Intron 5 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 4338AN: 91778Hom.: 372 Cov.: 23 FAILED QC
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GnomAD4 exome AF: 0.0795 AC: 73500AN: 924438Hom.: 24431 Cov.: 27 AF XY: 0.0845 AC XY: 38925AN XY: 460716
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0473 AC: 4345AN: 91836Hom.: 378 Cov.: 23 AF XY: 0.0465 AC XY: 2070AN XY: 44524
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Data not reliable, filtered out with message: AS_VQSR
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Not reported inComputational scores
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Prediction
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at