chr2:233682324:T>G Detail (hg38) (UGT1A, UGT1A10, UGT1A8, UGT1A7, UGT1A9)

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

Information

Genome

Assembly	Position
hg19	chr2:234,590,970-234,590,970 View the variant detail on this assembly version.
hg38	chr2:233,682,324-233,682,324

HGVS

Type	Transcript	Protein
RefSeq	NM_019075.2:c.855+44947T>G
Ensemble	ENST00000344644.10:c.855+44947T>G
	ENST00000373445.1:c.855+44947T>G

Type	Transcript	Protein
RefSeq	NM_019077.2:c.387T>G	NP_061950.2:p.Asn129Lys
Ensemble	ENST00000373426.4:c.387T>G	ENST00000373426.4:p.Asn129Lys

Type	Transcript	Protein
RefSeq	NM_019076.4:c.855+63762T>G
Ensemble	ENST00000373450.5:c.855+63762T>G

Type	Transcript	Protein
RefSeq	NM_021027.2:c.855+9535T>G
Ensemble	ENST00000354728.5:c.855+9535T>G

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.364
	ToMMo:0.375
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.411

Prediction

ClinVar

Clinical Significance	Benign
Review star
Show details

Links

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	tgv10917576	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	tgv10917576	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	tgv10917576	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	tgv10917576	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2023-11-30	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.129	liver carcinoma	Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, r...	BeFree	21240526	Detail
0.017	liver carcinoma	Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, r...	BeFree	21240526	Detail
0.030	liver carcinoma	Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, r...	BeFree	21240526	Detail
<0.001	Adenocarcinoma of pancreas	Pancreatic adenocarcinoma was associated with the low detoxification activity UG...	BeFree	12806614	Detail
0.005	Malignant neoplasm of liver	UGT1A7 polymorphisms were present in 93.2% of hepatocellular cancer patients, 74...	BeFree	11677206	Detail
<0.001	Malignant neoplasm of gastrointestinal tract	However, the UGT1A7*3 allele combining W208R, N129K and R131K missense mutations...	BeFree	12122597	Detail
<0.001	Colorectal cancer metastatic	Genotyping of the UGT1A1*28, UGT1A7 N129K/R131K, and UGT1A7-57T/G variants was d...	BeFree	18349289	Detail

Annotation

Annotations

Descrption	Source	Links
NM_019076.5(UGT1A8):c.855+63762T>G AND not provided	ClinVar	Detail
Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, rs2279744 of MDM2, rs...	DisGeNET	Detail
Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, rs2279744 of MDM2, rs...	DisGeNET	Detail
Six SNPs of five genes (rs1800562 of HFE, rs17868323 and rs11692021 of UGT1A7, rs2279744 of MDM2, rs...	DisGeNET	Detail
Pancreatic adenocarcinoma was associated with the low detoxification activity UGT1A7*3 allele, which...	DisGeNET	Detail
UGT1A7 polymorphisms were present in 93.2% of hepatocellular cancer patients, 74.5% carried the UGT1...	DisGeNET	Detail
However, the UGT1A7*3 allele combining W208R, N129K and R131K missense mutations and exhibiting subs...	DisGeNET	Detail
Genotyping of the UGT1A1*28, UGT1A7 N129K/R131K, and UGT1A7-57T/G variants was done in 105 irinoteca...	DisGeNET	Detail

Overlapped Transcript Coordinates

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs17868323 dbSNP
Genome: hg38
Position: chr2:233,682,324-233,682,324
Variant Type: snv
Reference Allele: T
Alternative Allele: G
Filtering Status (HGVD): PASS
Filtering Status (HGVD): VQSRTrancheSNP99.00to99.90
# of samples (HGVD): 1010
Mean of sample read depth (HGVD): 26.95
Standard deviation of sample read depth (HGVD): 29.33
Number of reference allele (HGVD): 1284
Number of alternative allele (HGVD): 736
Allele Frequency (HGVD): 0.36435643564356435
Gene Symbol (HGVD): UGT1A7
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)): rs17868323
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.3747
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 6280
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8550
East Asian Allele Counts (ExAC): 3518
East Asian Heterozygous Counts (ExAC): 2166
East Asian Homozygous Counts (ExAC): 676
East Asian Allele Frequency (ExAC): 0.4114619883040936
Chromosome Counts in All Race (ExAC): 119812
Allele Counts in All Race (ExAC): 70455
Heterozygous Counts in All Race (ExAC): 29131
Homozygous Counts in All Race (ExAC): 20662
Allele Frequency in All Race (ExAC): 0.5880462724935732

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