chr16:11249329:G>A Detail (hg19) (CLEC16A)

Information

Genome

Assembly Position
hg19 chr16:11,249,329-11,249,329
hg38 chr16:11,155,472-11,155,472 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_015226.2:c.2642-10916G>A
Ensemble ENST00000409790.6:c.2642-10916G>A
ENST00000703130.1:c.2636-10916G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.415
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 611303 OMIM
HGNC 29013 HGNC
Ensembl ENSG00000038532 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv54734952 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
0.006 rheumatoid arthritis The effect of the MHC2TA rs3087456G/rs4774C haplotype on RA susceptibility was c... BeFree 19221398 Detail
0.282 multiple sclerosis Independent genome-wide association studies highlighted the function of CLEC16A/... BeFree 19337309 Detail
0.281 Diabetes Mellitus, Insulin-Dependent Independent genome-wide association studies highlighted the function of CLEC16A/... BeFree 19337309 Detail
0.282 multiple sclerosis [Alleles of IL2RA and IL7RA and those in the HLA locus are identified as heritab... GAD 17660530 Detail
0.253 rheumatoid arthritis A novel association of rs6498169 with a predisposition to RA was described which... BeFree 19221398 Detail
Annotation

Annotations

DescrptionSourceLinks
The effect of the MHC2TA rs3087456G/rs4774C haplotype on RA susceptibility was confirmed, and the ha... DisGeNET Detail
Independent genome-wide association studies highlighted the function of CLEC16A/KIAA0350 polymorphis... DisGeNET Detail
Independent genome-wide association studies highlighted the function of CLEC16A/KIAA0350 polymorphis... DisGeNET Detail
[Alleles of IL2RA and IL7RA and those in the HLA locus are identified as heritable risk factors for ... DisGeNET Detail
A novel association of rs6498169 with a predisposition to RA was described which is consistent with ... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs6498169 dbSNP
Genome
hg19
Position
chr16:11,249,329-11,249,329
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))
rs6498169
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4152
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6958
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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