Nyuwa variants

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

Variant: 13-48045720-G-A(GRCh38)

Allele Count:	3
Allele Number:	5998
Allele Frequency:	5.0017e-4
Number of Homozygotes:	0

Reference:

dbSNP: rs147390019

gnomAD: 13-48045720-G-A

Browser:

Genotype Quality Metrics

Site Quality Metrics

External data population frequency

Dataset	Population	Population abbr	Allele Frequency
1KGP3	East Asian	EAS	1.0000e-3
	South Asian	SAS	0.0
	African	AFR	0.0
	Americas	AMR	7.2000e-3
	European ancestry	EUR	0.0
	total		1.1981e-3

gnomAD v3 Genomes	East Asian	EAS	1.5964e-3
	South Asian	SAS	0.0
	Afican	AFR	2.3798e-4
	Latino	AMR	0.0213
	Amish	AMI	0.0
	European(Finnish)	FIN	0.0
	European(non-Finnish)	NFE	6.1966e-5
	Ashkenazi Jewish	ASJ	0.0
	other	OTH	2.3256e-3
	total		2.1995e-3

Region annotation

	Region	Gene ID	Gene Detail	Exonic function	Consequence
Ensembl	exonic	NUDT15	-	unknown	UNKNOWN
RefSeq	exonic	NUDT15	-	nonsynonymous SNV	NUDT15:NM_018283:exon3:c.G416A:p.R139H

Nonsynonymous impact

Method	Score	Rank Score	predicted consequence
SIFT	0.38	0.112	T
PolyPhen2_HDIV	1.0	0.899	D
PolyPhen2_HVAR	0.871	0.601	P
FATHMM	2.49	0.145	T
CADD	4.715	0.632	24.6

Clinical annotation

ClinVar Significance	ClinVar Disease Name	ClinVar Allele ID	Tag-value
drug_response	Thiopurines,_poor_metabolism_of,_2	227130	MedGen:C4225160,OMIM:616903

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
NUDT15*4	thioguanine	TPMT, NUDT15 and Thiopurines	https://cpicpgx.org/guidelines/guideline-for-thiopurines-and-tpmt/	A	-	Testing recommended	21270794;23422873;30447069

Variant: 13-48045720-G-A(GRCh38)

Reference:

Browser: Browser

Genotype Quality Metrics

Site Quality Metrics

Browser: