chr2:234672639:G>T Detail (hg19) (UGT1A, UGT1A10, UGT1A8, UGT1A7, UGT1A6, UGT1A5, UGT1A9, UGT1A4, UGT1A1, UGT1A3)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

Assembly	Position
hg19	chr2:234,672,639-234,672,639
hg38	chr2:233,763,993-233,763,993 View the variant detail on this assembly version.

HGVS

Type	Transcript	Protein
RefSeq	NM_000463.2:c.864+2842G>T
Ensemble	ENST00000305208.10:c.864+2842G>T
	ENST00000360418.4:c.864+2842G>T

Type	Transcript	Protein
RefSeq	NM_019075.2:c.856-3041G>T
Ensemble	ENST00000344644.10:c.856-3041G>T
	ENST00000373445.1:c.856-3041G>T

Type	Transcript	Protein
RefSeq	NM_019093.2:c.868-3041G>T
Ensemble	ENST00000482026.6:c.868-3041G>T

Type	Transcript	Protein
RefSeq	NM_007120.2:c.868-3041G>T
Ensemble	ENST00000373409.8:c.868-3041G>T

Type	Transcript	Protein
RefSeq	NM_019078.1:c.868-3041G>T
Ensemble	ENST00000373414.4:c.868-3041G>T

Type	Transcript	Protein
RefSeq	NM_001072.3:c.862-3041G>T
	NM_205862.1:c.61-3041G>T
Ensemble	ENST00000305139.11:c.862-3041G>T
	ENST00000373424.5:c.61-3041G>T
	ENST00000406651.1:c.61-3041G>T

Type	Transcript	Protein
RefSeq	NM_019077.2:c.856-3041G>T
Ensemble	ENST00000373426.4:c.856-3041G>T

Type	Transcript	Protein
RefSeq	NM_019076.4:c.856-3041G>T
Ensemble	ENST00000373450.5:c.856-3041G>T

Type	Transcript	Protein
RefSeq	NM_021027.2:c.856-3041G>T
Ensemble	ENST00000354728.5:c.856-3041G>T

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:[No Data.]
	ToMMo:0.113
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance	Benign; association
Review star
Show details

Links

Type	Database	ID	Link
Gene	MIM	191740	OMIM
	HGNC	12530	HGNC
	Ensembl	ENSG00000241635	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv10920976	TogoVar
	COSMIC
	MONDO

Type	Database	ID	Link
Gene	MIM	606435	OMIM
	HGNC	12531	HGNC
	Ensembl	ENSG00000242515	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv10920976	TogoVar
	COSMIC
	MONDO

Type	Database	ID	Link
Gene	MIM	606428	OMIM
	HGNC	12535	HGNC
	Ensembl	ENSG00000288702	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv10920976	TogoVar
	COSMIC
	MONDO

Type	Database	ID	Link
Gene	MIM	606429	OMIM
	HGNC	12536	HGNC
	Ensembl	ENSG00000244474	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv10920976	TogoVar
	COSMIC
	MONDO

Type	Database	ID	Link
Gene	MIM	606430	OMIM
	HGNC	12537	HGNC
	Ensembl	ENSG00000288705	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv10920976	TogoVar
	COSMIC
	MONDO

Type	Database	ID	Link
Gene	MIM	606431	OMIM
	HGNC	12538	HGNC
	Ensembl	ENSG00000167165	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv10920976	TogoVar
	COSMIC
	MONDO

Type	Database	ID	Link
Gene	MIM	606432	OMIM
	HGNC	12539	HGNC
	Ensembl	ENSG00000244122	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv10920976	TogoVar
	COSMIC
	MONDO

Type	Database	ID	Link
Gene	MIM	606433	OMIM
	HGNC	12540	HGNC
	Ensembl	ENSG00000242366	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv10920976	TogoVar
	COSMIC
	MONDO

Type	Database	ID	Link
Gene	MIM	606434	OMIM
	HGNC	12541	HGNC
	Ensembl	ENSG00000241119	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv10920976	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
association	2009-07-15	no assertion criteria provided	Bilirubin, serum level of, quantitative trait locus 1	germline	Detail
Benign	2019-05-01	no assertion criteria provided	Gilbert syndrome	inherited	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.005	cholelithiasis	By using the presence of bilirubin as a phenotype, variants rs6742078 (UGT1A1; P...	BeFree	20837016	Detail
0.003	cholelithiasis	By using the presence of bilirubin as a phenotype, variants rs6742078 (UGT1A1; P...	BeFree	20837016	Detail
0.005	cholecystolithiasis	By using the presence of bilirubin as a phenotype, variants rs6742078 (UGT1A1; P...	BeFree	20837016	Detail
0.003	cholecystolithiasis	By using the presence of bilirubin as a phenotype, variants rs6742078 (UGT1A1; P...	BeFree	20837016	Detail
0.295	Gilbert Disease (disorder)	The UGT1A1 Gilbert syndrome variant rs6742078 is associated with gallstone disea...	BeFree	20837016	Detail
<0.001	Myocardial Ischemia	UGT1A1 rs6742078 TT versus GG genotype was associated with 95% increased bilirub...	BeFree	22805420	Detail
0.008	cholecystolithiasis	UGT1A1 (rs6742078; P = .018) was associated with overall gallstone risk.	BeFree	20837016	Detail
0.036	cholelithiasis	Second, taking advantage of mendelian randomization, we tested whether a genetic...	BeFree	23753274	Detail

Annotation

Annotations

Descrption	Source	Links
NM_000463.3(UGT1A1):c.864+2842G>T AND Bilirubin, serum level of, quantitative trait locus 1	ClinVar	Detail
NM_000463.3(UGT1A1):c.864+2842G>T AND Gilbert syndrome	ClinVar	Detail
By using the presence of bilirubin as a phenotype, variants rs6742078 (UGT1A1; P = .003), rs4149056 ...	DisGeNET	Detail
By using the presence of bilirubin as a phenotype, variants rs6742078 (UGT1A1; P = .003), rs4149056 ...	DisGeNET	Detail
By using the presence of bilirubin as a phenotype, variants rs6742078 (UGT1A1; P = .003), rs4149056 ...	DisGeNET	Detail
By using the presence of bilirubin as a phenotype, variants rs6742078 (UGT1A1; P = .003), rs4149056 ...	DisGeNET	Detail
The UGT1A1 Gilbert syndrome variant rs6742078 is associated with gallstone disease in men; further s...	DisGeNET	Detail
UGT1A1 rs6742078 TT versus GG genotype was associated with 95% increased bilirubin levels (P < 0....	DisGeNET	Detail
UGT1A1 (rs6742078; P = .018) was associated with overall gallstone risk.	DisGeNET	Detail
Second, taking advantage of mendelian randomization, we tested whether a genetic variant in the bili...	DisGeNET	Detail

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs6742078 dbSNP
Genome: hg19
Position: chr2:234,672,639-234,672,639
Variant Type: snv
Reference Allele: G
Alternative Allele: T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): rs6742078
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.1131
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 1896
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760

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