chr1:177913519:T>C Detail (hg19) (SEC16B)

Information

Genome

Assembly Position
hg19 chr1:177,913,519-177,913,519
hg38 chr1:177,944,384-177,944,384 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_033127.2:c.1881+177A>G
Ensemble ENST00000308284.11:c.1881+177A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.232
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 612855 OMIM
HGNC 30301 HGNC
Ensembl ENSG00000120341 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv3896318 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
0.003 obesity Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nom... BeFree 23121087 Detail
0.021 obesity Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nom... BeFree 23121087 Detail
0.153 obesity Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nom... BeFree 23121087 Detail
0.162 obesity The SNP rs10913469 in SEC16B (P=0.000012) and four SNPs (rs2867125, rs6548238, r... BeFree 19851340 Detail
0.278 obesity Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nom... BeFree 23121087 Detail
Annotation

Annotations

DescrptionSourceLinks
Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nominally associated wi... DisGeNET Detail
Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nominally associated wi... DisGeNET Detail
Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nominally associated wi... DisGeNET Detail
The SNP rs10913469 in SEC16B (P=0.000012) and four SNPs (rs2867125, rs6548238, rs4854344 and rs75613... DisGeNET Detail
Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nominally associated wi... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs10913469 dbSNP
Genome
hg19
Position
chr1:177,913,519-177,913,519
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))
rs10913469
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2317
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3884
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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