chr18:12835976:T>C Detail (hg19) (PTPN2)

Information

Genome

Assembly Position
hg19 chr18:12,835,976-12,835,976
hg38 chr18:12,835,977-12,835,977 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002828.3:c.261+814A>G
NM_080422.2:c.261+814A>G
NM_080423.2:c.261+814A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.154
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 tgv59301175 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
0.371 Diabetes Mellitus, Insulin-Dependent Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs115... BeFree 22960018 Detail
0.020 Diabetes Mellitus, Insulin-Dependent Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs115... BeFree 22960018 Detail
Annotation

Annotations

DescrptionSourceLinks
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932... DisGeNET Detail
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs478582 dbSNP
Genome
hg19
Position
chr18:12,835,976-12,835,976
Variant Type
snv
Reference Allele
T
Alternative Allele
C
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))
rs478582
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1543
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2586
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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