chr2:240878099:A>G Detail (hg38) (AGXT)

Information

Genome

Assembly Position
hg19 chr2:241,817,516-241,817,516 View the variant detail on this assembly version.
hg38 chr2:240,878,099-240,878,099

HGVS

Type Transcript Protein
RefSeq NM_000030.2:c.1020A>G NP_000021.1:p.Ile340Met
Ensemble ENST00000307503.4:c.1020A>G ENST00000307503.4:p.Ile340Met
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.083
ToMMo:0.068
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.086

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 604285 OMIM
HGNC 341 HGNC
Ensembl ENSG00000172482 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv11122592 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2021-11-17 criteria provided, multiple submitters, no conflicts Primary hyperoxaluria, type I germline unknown Detail
Benign 2016-06-26 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.579 Primary hyperoxaluria, type I The G170R variant of the alanine:glyoxylate aminotransferase (AGT) is the most c... BeFree 21103899 Detail
0.579 Primary hyperoxaluria, type I NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000030.3(AGXT):c.1020A>G (p.Ile340Met) AND Primary hyperoxaluria, type I ClinVar Detail
NM_000030.3(AGXT):c.1020A>G (p.Ile340Met) AND not specified ClinVar Detail
NM_000030.3(AGXT):c.1020A>G (p.Ile340Met) AND not provided ClinVar Detail
The G170R variant of the alanine:glyoxylate aminotransferase (AGT) is the most common pathogenic all... DisGeNET Detail
NA 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
rs4426527 dbSNP
Genome
hg38
Position
chr2:240,878,099-240,878,099
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
75.45
Standard deviation of sample read depth (HGVD)
37.23
Number of reference allele (HGVD)
2215
Number of alternative allele (HGVD)
201
Allele Frequency (HGVD)
0.08319536423841059
Gene Symbol (HGVD)
AGXT
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))
rs4426527
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0681
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1142
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8572
East Asian Allele Counts (ExAC)
737
East Asian Heterozygous Counts (ExAC)
691
East Asian Homozygous Counts (ExAC)
23
East Asian Allele Frequency (ExAC)
0.08597760149323379
Chromosome Counts in All Race (ExAC)
120178
Allele Counts in All Race (ExAC)
19861
Heterozygous Counts in All Race (ExAC)
16067
Homozygous Counts in All Race (ExAC)
1897
Allele Frequency in All Race (ExAC)
0.16526319293048644
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