chr15:78593646:T>C Detail (hg38) (CHRNA3, CHRNA5)

Information

Genome

Assembly Position
hg19 chr15:78,885,988-78,885,988 View the variant detail on this assembly version.
hg38 chr15:78,593,646-78,593,646

HGVS

Type Transcript Protein
RefSeq NM_001166694.1:c.1390-455A>G
Ensemble ENST00000348639.7:c.1390-455A>G
Type Transcript Protein
RefSeq NM_000745.3:c.*393T>C
Ensemble ENST00000299565.9:c.*393T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.876
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 118503 OMIM
HGNC 1957 HGNC
Ensembl ENSG00000080644 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv53652758 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 118505 OMIM
HGNC 1959 HGNC
Ensembl ENSG00000169684 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv53652758 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
0.133 Alcoholic Intoxication, Chronic We also observed two SNPs associated with alcohol dependence, that is, rs615470 ... BeFree 20485328 Detail
Annotation

Annotations

DescrptionSourceLinks
We also observed two SNPs associated with alcohol dependence, that is, rs615470 in CHRNA5 (OR=0.77, ... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs615470 dbSNP
Genome
hg38
Position
chr15:78,593,646-78,593,646
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))
rs615470
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8764
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
14689
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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