chr5:1320722:C>T Detail (hg19) (CLPTM1L)

Information

Genome

Assembly Position
hg19 chr5:1,320,722-1,320,722
hg38 chr5:1,320,607-1,320,607 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_030782.4:c.1532+9G>A
Ensemble ENST00000320895.10:c.1532+9G>A
ENST00000507807.3:c.1025+9G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.318
ToMMo:0.323
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.331

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 612585 OMIM
HGNC 24308 HGNC
Ensembl ENSG00000049656 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv20012873 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
0.001 Nasopharyngeal carcinoma Four out of six genetic variants implicated in the recent NPC GWAS were associat... BeFree 23085811 Detail
0.009 Carcinoma of lung Association between CLPTM1L polymorphisms (rs402710 and rs401681) and lung cance... BeFree 24907075 Detail
0.143 Malignant neoplasm of lung Association between CLPTM1L polymorphisms (rs402710 and rs401681) and lung cance... BeFree 24907075 Detail
0.135 Lung Neoplasms [Lung cancer susceptibility locus at 5p15.33.] GAD 18978790 Detail
0.143 Malignant neoplasm of lung [The susceptibility region contains two genes, TERT and CLPTM1L, suggesting that... GAD 18978790 Detail
0.155 Malignant neoplasm of lung [The susceptibility region contains two genes, TERT and CLPTM1L, suggesting that... GAD 18978790 Detail
Annotation

Annotations

DescrptionSourceLinks
Four out of six genetic variants implicated in the recent NPC GWAS were associated with NPC risk (p ... DisGeNET Detail
Association between CLPTM1L polymorphisms (rs402710 and rs401681) and lung cancer susceptibility: ev... DisGeNET Detail
Association between CLPTM1L polymorphisms (rs402710 and rs401681) and lung cancer susceptibility: ev... DisGeNET Detail
[Lung cancer susceptibility locus at 5p15.33.] DisGeNET Detail
[The susceptibility region contains two genes, TERT and CLPTM1L, suggesting that one or both may hav... DisGeNET Detail
[The susceptibility region contains two genes, TERT and CLPTM1L, suggesting that one or both may hav... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg19
Position
chr5:1,320,722-1,320,722
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
964
Mean of sample read depth (HGVD)
21.29
Standard deviation of sample read depth (HGVD)
8.63
Number of reference allele (HGVD)
1315
Number of alternative allele (HGVD)
613
Allele Frequency (HGVD)
0.3179460580912863
Gene Symbol (HGVD)
CLPTM1L
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))
rs402710
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3234
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5420
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
616
East Asian Allele Counts (ExAC)
204
East Asian Heterozygous Counts (ExAC)
132
East Asian Homozygous Counts (ExAC)
36
East Asian Allele Frequency (ExAC)
0.33116883116883117
Chromosome Counts in All Race (ExAC)
18652
Allele Counts in All Race (ExAC)
6456
Heterozygous Counts in All Race (ExAC)
4330
Homozygous Counts in All Race (ExAC)
1063
Allele Frequency in All Race (ExAC)
0.3461291014368432
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