chr2:233283605:C>T Detail (hg38) (ATG16L1)

Information

Genome

Assembly Position
hg19 chr2:234,192,251-234,192,251 View the variant detail on this assembly version.
hg38 chr2:233,283,605-233,283,605

HGVS

Type Transcript Protein
RefSeq NM_198890.2:c.714+852C>T
NM_001190266.1:c.1203+852C>T
NM_001190267.1:c.1203+852C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.185
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

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 tgv10904687 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
Annotation

Annotations

DescrptionSourceLinks
Epistasis analysis showed weak epistasis between the ATG16L1 SNP rs2241879 and PTPN2 SNP rs2542151 (... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs4663396 dbSNP
Genome
hg38
Position
chr2:233,283,605-233,283,605
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs4663396
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1851
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3103
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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