chr3:126107216:T>C Detail (hg38) (ALDH1L1)

Information

Genome

Assembly Position
hg19 chr3:125,826,059-125,826,059 View the variant detail on this assembly version.
hg38 chr3:126,107,216-126,107,216

HGVS

Type Transcript Protein
RefSeq NM_001270364.1:c.2408A>G NP_001257293.1:p.Asp803Gly
NR_072979.1:c.*609A>G
NM_012190.3:c.2378A>G NP_036322.2:p.Asp793Gly
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.124
ToMMo:0.123
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.134

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600249 OMIM
HGNC 3978 HGNC
Ensembl ENSG00000144908 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv14096364 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Lymphoma, Large-Cell, Follicular A significantly reduced risk of NHL was associated with the homozygous TT genoty... BeFree 23913011 Detail
<0.001 Lymphoma, Large-Cell, Follicular A significantly reduced risk of NHL was associated with the homozygous TT genoty... BeFree 23913011 Detail
0.006 Lymphoma, Non-Hodgkin A significantly reduced risk of NHL was associated with the homozygous TT genoty... BeFree 23913011 Detail
<0.001 Lymphoma, Large-Cell, Follicular A significantly reduced risk of NHL was associated with the homozygous TT genoty... BeFree 23913011 Detail
<0.001 Lymphoma, Non-Hodgkin A significantly reduced risk of NHL was associated with the homozygous TT genoty... BeFree 23913011 Detail
0.006 Lymphoma, Non-Hodgkin A significantly reduced risk of NHL was associated with the homozygous TT genoty... BeFree 23913011 Detail
<0.001 liver carcinoma Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTH... BeFree 25318605 Detail
<0.001 liver carcinoma Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTH... BeFree 25318605 Detail
Annotation

Annotations

DescrptionSourceLinks
A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... DisGeNET Detail
A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... DisGeNET Detail
A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... DisGeNET Detail
A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... DisGeNET Detail
A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... DisGeNET Detail
A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... DisGeNET Detail
Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTHFD rs1127717, GART r... DisGeNET Detail
Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTHFD rs1127717, GART r... 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
-
Genome
hg38
Position
chr3:126,107,216-126,107,216
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
158.80
Standard deviation of sample read depth (HGVD)
77.54
Number of reference allele (HGVD)
2119
Number of alternative allele (HGVD)
299
Allele Frequency (HGVD)
0.12365591397849462
Gene Symbol (HGVD)
ALDH1L1
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))
rs1127717
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1232
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2064
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8622
East Asian Allele Counts (ExAC)
1157
East Asian Heterozygous Counts (ExAC)
1015
East Asian Homozygous Counts (ExAC)
71
East Asian Allele Frequency (ExAC)
0.13419160287636278
Chromosome Counts in All Race (ExAC)
121318
Allele Counts in All Race (ExAC)
22886
Heterozygous Counts in All Race (ExAC)
18258
Homozygous Counts in All Race (ExAC)
2314
Allele Frequency in All Race (ExAC)
0.18864471883809492
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