chr18:12877060:A>G Detail (hg19) (PTPN2)

Information

Genome

Assembly Position
hg19 chr18:12,877,060-12,877,060
hg38 chr18:12,877,061-12,877,061 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002828.3:c.69+7012T>C
NM_080422.2:c.69+7012T>C
NM_080423.2:c.69+7012T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.365
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 176887 OMIM
HGNC 9650 HGNC
Ensembl ENSG00000175354 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv59302183 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
0.124 Inflammatory Bowel Diseases Genomic DNA from 2131 individuals of Caucasian origin (905 patients with CD, 318... BeFree 22457781 Detail
Annotation

Annotations

DescrptionSourceLinks
Epistasis analysis showed weak epistasis between the ATG16L1 SNP rs2241879 and PTPN2 SNP rs2542151 (... DisGeNET Detail
Genomic DNA from 2131 individuals of Caucasian origin (905 patients with CD, 318 patients with UC, a... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs7234029 dbSNP
Genome
hg19
Position
chr18:12,877,060-12,877,060
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs7234029
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3652
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6121
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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