Variant: 22-42129819-G-T(GRCh38)

Allele Count: 17
Allele Number: 5978
Allele Frequency: 2.8438e-3
Number of Homozygotes: 0

Reference:

dbSNP: rs28371703

gnomAD: 22-42129819-G-T

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Genotype Quality Metrics

Site Quality Metrics

External data population frequency
DatasetPopulationPopulation abbrAllele Frequency
1KGP3East AsianEAS1.0000e-3
South AsianSAS0.0808
AfricanAFR0.0204
AmericasAMR0.0951
European ancestryEUR0.1730
total0.0693
gnomAD v3 GenomesEast AsianEAS2.2494e-3
South AsianSAS0.0885
AficanAFR0.0384
LatinoAMR0.1024
AmishAMI0.2290
European(Finnish)FIN0.0921
European(non-Finnish)NFE0.1920
Ashkenazi JewishASJ0.1832
otherOTH0.1264
total0.1239

Region annotation
RegionGene IDGene DetailExonic functionConsequence
EnsemblexonicCYP2D6-nonsynonymous SNVCYP2D6:ENST00000359033.4:exon2:c.C271A:p.L91M,CYP2D6:ENST00000389970.7:exon2:c.C205A:p.L69M
RefSeqexonicCYP2D6;CYP2D7-nonsynonymous SNVCYP2D6:NM_000106:exon2:c.C271A:p.L91M,CYP2D6:NM_001025161:exon2:c.C271A:p.L91M

Nonsynonymous impact
MethodScoreRank Scorepredicted consequence
SIFT0.0390.469D
PolyPhen2_HDIV0.5810.398P
PolyPhen2_HVAR0.8390.595P
FATHMM-0.940.753T
CADD3.5080.47923.1

Clinical annotation
ClinVar SignificanceClinVar Disease NameClinVar Allele IDTag-value
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Loss of function predict

Loss of Function (LoF) variants are indentified by package LOFTEE developed recently by gnomAD group to assess stop-gained, splice site disrupting and frameshift variants as “low-confidence” (LC) or “high-confidence” (HC) LoF variants.

LoFLoF_filterLoF_flagsLoF_info
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Pharmacogenomics
Belong to HaplotypeDrugGuideineURLCPIC_LevelPharmGKB_Level_of_EvidencePGx_on_
FDA_Label
CPIC_Publications
_PMID
CYP2D6*4atomoxetineCYP2D6 and Atomoxetinehttps://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/A1AActionable PGx30801677
CYP2D6*4codeineCYP2D6 and Codeinehttps://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/A1AActionable PGx22205192;24458010
CYP2D6*4ondansetronCYP2D6 and Ondansetron and Tropisetronhttps://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/A1AInformative PGx28002639
CYP2D6*4tamoxifenCYP2D6 and Tamoxifenhttps://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/A1AActionable PGx29385237
CYP2D6*4fluvoxamineCYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitorshttps://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/A1AActionable PGx25974703
CYP2D6*4clomipramineCYP2D6, CYP2C19 and Tricyclic Antidepressantshttps://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/B1AActionable PGx23486447;27997040
CYP2D6*74atomoxetineCYP2D6 and Atomoxetinehttps://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/A1AActionable PGx30801677
CYP2D6*74codeineCYP2D6 and Codeinehttps://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/A1AActionable PGx22205192;24458010
CYP2D6*74ondansetronCYP2D6 and Ondansetron and Tropisetronhttps://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/A1AInformative PGx28002639
CYP2D6*74tamoxifenCYP2D6 and Tamoxifenhttps://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/A1AActionable PGx29385237
CYP2D6*74fluvoxamineCYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitorshttps://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/A1AActionable PGx25974703
CYP2D6*74clomipramineCYP2D6, CYP2C19 and Tricyclic Antidepressantshttps://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/B1AActionable PGx23486447;27997040
CYP2D6*82atomoxetineCYP2D6 and Atomoxetinehttps://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/A1AActionable PGx30801677
CYP2D6*82codeineCYP2D6 and Codeinehttps://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/A1AActionable PGx22205192;24458010
CYP2D6*82ondansetronCYP2D6 and Ondansetron and Tropisetronhttps://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/A1AInformative PGx28002639
CYP2D6*82tamoxifenCYP2D6 and Tamoxifenhttps://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/A1AActionable PGx29385237
CYP2D6*82fluvoxamineCYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitorshttps://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/A1AActionable PGx25974703
CYP2D6*82clomipramineCYP2D6, CYP2C19 and Tricyclic Antidepressantshttps://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/B1AActionable PGx23486447;27997040