chr20:3193893:A>C Detail (hg19) (ITPA)

Information

Genome

Assembly Position
hg19 chr20:3,193,893-3,193,893
hg38 chr20:3,213,247-3,213,247 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001324236.1:c.124+21A>C
NM_001324237.1:c.124+21A>C
NM_001324240.1:c.124+21A>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance drug response
Review star
Show details
Links
Type Database ID Link
Gene MIM 147520 OMIM
HGNC 6176 HGNC
Ensembl ENSG00000125877 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62926837 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-22 criteria provided, single submitter Inosine triphosphatase deficiency germline Detail
Benign 2021-05-12 criteria provided, single submitter not provided germline Detail
Benign 2021-08-19 criteria provided, single submitter Developmental and epileptic encephalopathy, 35 germline Detail
drug response 2021-03-24 reviewed by expert panel germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.128 Hepatitis C, Chronic ITPA gene variants protect against anaemia in patients treated for chronic hepat... GWASCAT 20173735 Detail
<0.001 Coinfection The role of rs1127354/rs7270101 alleles at the inosine triphosphatase (ITPA) gen... BeFree 22028438 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_033453.4(ITPA):c.124+21A>C AND Inosine triphosphatase deficiency ClinVar Detail
NM_033453.4(ITPA):c.124+21A>C AND not provided ClinVar Detail
NM_033453.4(ITPA):c.124+21A>C AND Developmental and epileptic encephalopathy, 35 ClinVar Detail
NM_033453.4(ITPA):c.124+21A>C AND peginterferon alfa-2b and ribavirin response - Toxicity ClinVar Detail
ITPA gene variants protect against anaemia in patients treated for chronic hepatitis C. DisGeNET Detail
The role of rs1127354/rs7270101 alleles at the inosine triphosphatase (ITPA) gene on ribavirin-induc... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs7270101 dbSNP
Genome
hg19
Position
chr20:3,193,893-3,193,893
Variant Type
snv
Reference Allele
A
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
184.74
Standard deviation of sample read depth (HGVD)
77.46
Number of reference allele (HGVD)
1672
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
0.0011947431302270011
Gene Symbol (HGVD)
ITPA
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))
rs7270101
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
1
East Asian Heterozygous Counts (ExAC)
1
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
1.1555350127108852E-4
Chromosome Counts in All Race (ExAC)
121398
Allele Counts in All Race (ExAC)
10760
Heterozygous Counts in All Race (ExAC)
9552
Homozygous Counts in All Race (ExAC)
604
Allele Frequency in All Race (ExAC)
0.08863407963887379
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