chr2:234183468:G>A Detail (hg19) (ATG16L1)

Information

Genome

Assembly Position
hg19 chr2:234,183,468-234,183,468
hg38 chr2:233,274,822-233,274,822 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_198890.2:c.465+44G>A
NM_001190266.1:c.954+44G>A
NM_001190267.1:c.954+44G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.220
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.333

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 610767 OMIM
HGNC 21498 HGNC
Ensembl ENSG00000085978 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv10904400 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
0.033 ulcerative colitis Epistasis analysis showed weak epistasis between the ATG16L1 SNP rs2241879 and P... BeFree 22457781 Detail
0.368 Crohn Disease The ATG16L1 gene variants rs2241879 and rs2241880 (T300A) are strongly associate... BeFree 18162085 Detail
Annotation

Annotations

DescrptionSourceLinks
Epistasis analysis showed weak epistasis between the ATG16L1 SNP rs2241879 and PTPN2 SNP rs2542151 (... DisGeNET Detail
The ATG16L1 gene variants rs2241879 and rs2241880 (T300A) are strongly associated with susceptibilit... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2241879 dbSNP
Genome
hg19
Position
chr2:234,183,468-234,183,468
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs2241879
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2202
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3690
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8348
East Asian Allele Counts (ExAC)
2782
East Asian Heterozygous Counts (ExAC)
1928
East Asian Homozygous Counts (ExAC)
427
East Asian Allele Frequency (ExAC)
0.3332534738859607
Chromosome Counts in All Race (ExAC)
117134
Allele Counts in All Race (ExAC)
53591
Heterozygous Counts in All Race (ExAC)
27871
Homozygous Counts in All Race (ExAC)
12860
Allele Frequency in All Race (ExAC)
0.457518739221746
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