chr15:78595490:A>G Detail (hg38) (CHRNA3)

Information

Genome

Assembly Position
hg19 chr15:78,887,832-78,887,832 View the variant detail on this assembly version.
hg38 chr15:78,595,490-78,595,490

HGVS

Type Transcript Protein
RefSeq NM_000743.4:c.*1114T>C
NM_001166694.1:c.1390-2299T>C
Ensemble ENST00000326828.6:c.*1114T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.877
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 tgv53652804 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 Lung Diseases, Obstructive Two single-nucleotide polymorphisms (SNPs) in CHRNA3 (rs660652 and rs12910984) w... BeFree 23207642 Detail
<0.001 nicotine dependence Single-nucleotide polymorphisms rs421629 on 5p15.33 and rs1948, rs660652, rs8040... BeFree 22945651 Detail
0.015 Carcinoma of lung Single-nucleotide polymorphisms rs421629 on 5p15.33 and rs1948, rs660652, rs8040... BeFree 22945651 Detail
0.155 Malignant neoplasm of lung Single-nucleotide polymorphisms rs421629 on 5p15.33 and rs1948, rs660652, rs8040... BeFree 22945651 Detail
0.133 nicotine dependence In pairwise interaction analysis of SNPs from the two loci (COMT SNP-CHRNA5-CHRN... BeFree 21312287 Detail
0.020 nicotine dependence In pairwise interaction analysis of SNPs from the two loci (COMT SNP-CHRNA5-CHRN... BeFree 21312287 Detail
Annotation

Annotations

DescrptionSourceLinks
Two single-nucleotide polymorphisms (SNPs) in CHRNA3 (rs660652 and rs12910984) were genotyped in 219... DisGeNET Detail
Single-nucleotide polymorphisms rs421629 on 5p15.33 and rs1948, rs660652, rs8040868 and rs2036527 on... DisGeNET Detail
Single-nucleotide polymorphisms rs421629 on 5p15.33 and rs1948, rs660652, rs8040868 and rs2036527 on... DisGeNET Detail
Single-nucleotide polymorphisms rs421629 on 5p15.33 and rs1948, rs660652, rs8040868 and rs2036527 on... DisGeNET Detail
In pairwise interaction analysis of SNPs from the two loci (COMT SNP-CHRNA5-CHRNA3 SNP), the interac... DisGeNET Detail
In pairwise interaction analysis of SNPs from the two loci (COMT SNP-CHRNA5-CHRNA3 SNP), the interac... 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
rs660652 dbSNP
Genome
hg38
Position
chr15:78,595,490-78,595,490
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs660652
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8766
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
14692
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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