Nyuwa variants

Basic
Quality Metrics
External data
Region Annotation
Nonsynonymous impact
Loss of function predict
Clinical annotation
Pharmacogenomics

Variant: 22-42128694-T-C(GRCh38)

Allele Count:	3167
Allele Number:	5976
Allele Frequency:	0.5300
Number of Homozygotes:	926

Reference:

dbSNP: rs2267447

gnomAD: 22-42128694-T-C

Browser:

Genotype Quality Metrics

Site Quality Metrics

External data population frequency

Dataset	Population	Population abbr	Allele Frequency
1KGP3	East Asian	EAS	0.58
	South Asian	SAS	0.1605
	African	AFR	0.1233
	Americas	AMR	0.1484
	European ancestry	EUR	0.2008
	total		0.2406

gnomAD v3 Genomes	East Asian	EAS	0.5730
	South Asian	SAS	0.1765
	Afican	AFR	0.1321
	Latino	AMR	0.1531
	Amish	AMI	0.2993
	European(Finnish)	FIN	0.1118
	European(non-Finnish)	NFE	0.2227
	Ashkenazi Jewish	ASJ	0.2412
	other	OTH	0.2012
	total		0.1890

Region annotation

	Region	Gene ID	Gene Detail	Exonic function	Consequence
Ensembl	ncRNA_intronic	NDUFA6-AS1	-	-	-
RefSeq	ncRNA_intronic	LOC101929829	-	-	-

Nonsynonymous impact

Method	Score	Rank Score	predicted consequence
SIFT	-	-	-
PolyPhen2_HDIV	-	-	-
PolyPhen2_HVAR	-	-	-
FATHMM	-	-	-
CADD	-	-	-

Clinical annotation

ClinVar Significance	ClinVar Disease Name	ClinVar Allele ID	Tag-value
-	-	-	-

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.

LoF	LoF_filter	LoF_flags	LoF_info
-	-	-	-

Pharmacogenomics

Belong to Haplotype	Drug	Guideine	URL	CPIC_Level	PharmGKB_Level_of_Evidence	PGx_on_ FDA_Label	CPIC_Publications _PMID
CYP2D6*100	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*100	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*100	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*100	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*100	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*100	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040
CYP2D6*101	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*101	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*101	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*101	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*101	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*101	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040
CYP2D6*10	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*10	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*10	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*10	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*10	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*10	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040
CYP2D6*36	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*36	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*36	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*36	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*36	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*36	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040
CYP2D6*4	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*4	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*4	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*4	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*4	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*4	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040
CYP2D6*52	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*52	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*52	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*52	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*52	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*52	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040
CYP2D6*56	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*56	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*56	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*56	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*56	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*56	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040
CYP2D6*64	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*64	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*64	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*64	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*64	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*64	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040
CYP2D6*72	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*72	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*72	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*72	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*72	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*72	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040
CYP2D6*99	atomoxetine	CYP2D6 and Atomoxetine	https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	30801677
CYP2D6*99	codeine	CYP2D6 and Codeine	https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/	A	1A	Actionable PGx	22205192;24458010
CYP2D6*99	ondansetron	CYP2D6 and Ondansetron and Tropisetron	https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/	A	1A	Informative PGx	28002639
CYP2D6*99	tamoxifen	CYP2D6 and Tamoxifen	https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/	A	1A	Actionable PGx	29385237
CYP2D6*99	fluvoxamine	CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors	https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/	A	1A	Actionable PGx	25974703
CYP2D6*99	clomipramine	CYP2D6, CYP2C19 and Tricyclic Antidepressants	https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/	B	1A	Actionable PGx	23486447;27997040

Variant: 22-42128694-T-C(GRCh38)

Reference:

Browser: Browser

Genotype Quality Metrics

Site Quality Metrics

Browser: