chr3:169082633:G>A Detail (hg19) (MECOM)

Information

Genome

Assembly Position
hg19 chr3:169,082,633-169,082,633
hg38 chr3:169,364,845-169,364,845 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_004991.3:c.375+16342C>T
Ensemble ENST00000494292.6:c.375+16342C>T
ENST00000651503.2:c.375+16342C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.591
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 165215 OMIM
HGNC 3498 HGNC
Ensembl ENSG00000085276 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv15051080 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
0.121 Nasopharyngeal carcinoma Three SNPs (rs401681, rs6774494 and rs3757318) corresponding to TERT/CLPTM1L (OR... BeFree 24615621 Detail
<0.001 Nasopharyngeal carcinoma Three SNPs (rs401681, rs6774494 and rs3757318) corresponding to TERT/CLPTM1L (OR... BeFree 24615621 Detail
0.121 Nasopharyngeal carcinoma Our findings provide new insights into the pathogenesis of NPC by highlighting t... GWASCAT 20512145 Detail
0.122 Nasopharyngeal Neoplasms [A genome-wide association study of nasopharyngeal carcinoma identifies three ne... GAD 20512145 Detail
Annotation

Annotations

DescrptionSourceLinks
Three SNPs (rs401681, rs6774494 and rs3757318) corresponding to TERT/CLPTM1L (OR 95% CI = 0.77, 0.68... DisGeNET Detail
Three SNPs (rs401681, rs6774494 and rs3757318) corresponding to TERT/CLPTM1L (OR 95% CI = 0.77, 0.68... DisGeNET Detail
Our findings provide new insights into the pathogenesis of NPC by highlighting the involvement of pa... DisGeNET Detail
[A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loc... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs6774494 dbSNP
Genome
hg19
Position
chr3:169,082,633-169,082,633
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))
rs6774494
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5912
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9908
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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