chr15:78601997:G>A Detail (hg38) (CHRNA3)

Information

Genome

Assembly Position
hg19 chr15:78,894,339-78,894,339 View the variant detail on this assembly version.
hg38 chr15:78,601,997-78,601,997

HGVS

Type Transcript Protein
RefSeq NM_000743.4:c.645C>T NP_000734.2:p.Tyr215=
NM_001166694.1:c.645C>T NP_001160166.1:p.Tyr215=
Ensemble ENST00000326828.6:c.645C>T ENST00000326828.6:p.Tyr215=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.019
ToMMo:0.021
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.031

Prediction

ClinVar

Clinical Significance Benign
Review star
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 tgv53653172 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2008-05-01 no assertion criteria provided Lung cancer susceptibility 2 germline Detail
risk factor 2008-05-01 no assertion criteria provided Smoking as a quantitative trait locus 3 germline Detail
Benign 2024-01-30 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.179 Malignant neoplasm of lung Associations of SNPs in LOC123688 (rs10519203; odds ratio [OR] = 1.60, 95% confi... BeFree 20554942 Detail
0.133 nicotine dependence In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we ... BeFree 19247474 Detail
<0.001 Drug habituation We assessed the effect of nicotine on PPI, startle reactivity, and habituation i... BeFree 23604333 Detail
<0.001 cannabis abuse Rs16969968 in CHRNA5 (and its proxy, rs1051730 in CHRNA3) and rs1451240, a proxy... BeFree 25770649 Detail
0.120 LUNG CANCER SUSCEPTIBILITY 2 (disorder) NA CLINVAR Detail
0.002 Carcinoma of lung Our findings demonstrated that CHRNA3 gene rs1051730-A allele and AGPHD1 gene rs... BeFree 22701590 Detail
0.129 Chronic Obstructive Airway Disease In ever-smokers, the CHRNA3 rs1051730 genotype associated with reduced lung func... BeFree 22441734 Detail
0.010 Carcinoma of lung Associations of SNPs in LOC123688 (rs10519203; odds ratio [OR] = 1.60, 95% confi... BeFree 20554942 Detail
0.020 nicotine dependence In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we ... BeFree 19247474 Detail
0.133 nicotine dependence Moreover, the TT genotype of the nicotinic acetylcholine receptor (nAChR) α3-sub... BeFree 23604333 Detail
0.012 Carcinoma of lung In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we ... BeFree 19247474 Detail
0.133 nicotine dependence A variant associated with nicotine dependence, lung cancer and peripheral arteri... GWASCAT 18385739 Detail
0.120 SMOKING AS A QUANTITATIVE TRAIT LOCUS 3 (disorder) NA CLINVAR Detail
0.179 Malignant neoplasm of lung We also investigated the relationship between the rs1051730 SNP in an intron of ... BeFree 21645942 Detail
0.123 Adenocarcinoma of lung (disorder) A genome-wide association study of lung cancer identifies a region of chromosome... GWASCAT 19836008 Detail
<0.001 obesity A genetic variant within the CHRNA5-CHRNA3-CHRNB4 region (rs1051730), previously... BeFree 23729684 Detail
0.123 Adenocarcinoma of lung (disorder) [a lung cancer GWAS identified a distinct hereditary contribution to adenocarcin... GAD 19836008 Detail
0.010 Carcinoma of lung Our findings demonstrated that CHRNA3 gene rs1051730-A allele and AGPHD1 gene rs... BeFree 22701590 Detail
0.010 Carcinoma of lung Similarly, neither CHRNA3 rs8034191 nor rs1051730 were associated with lung canc... BeFree 20068085 Detail
0.011 nicotine dependence [A variant associated with nicotine dependence, lung cancer and peripheral arter... GAD 18385739 Detail
0.133 nicotine dependence [A variant associated with nicotine dependence, lung cancer and peripheral arter... GAD 18385739 Detail
0.020 nicotine dependence A recent genome-wide association study demonstrated an association between a com... BeFree 19429911 Detail
<0.001 Chronic Obstructive Airway Disease Our findings suggest that rs1051730 in CHRNA is a susceptibility variant for COP... BeFree 22176972 Detail
0.010 Carcinoma of lung Association between CHRNA3 rs1051730 genotype and lung cancer risk in Chinese Ha... BeFree 24337855 Detail
<0.001 nicotine dependence In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we ... BeFree 19247474 Detail
<0.001 cannabis abuse Rs16969968 in CHRNA5 (and its proxy, rs1051730 in CHRNA3) and rs1451240, a proxy... BeFree 25770649 Detail
0.179 Malignant neoplasm of lung Association between CHRNA3 rs1051730 genotype and lung cancer risk in Chinese Ha... BeFree 24337855 Detail
0.011 nicotine dependence A recent genome-wide association study demonstrated an association between a com... BeFree 19429911 Detail
0.134 Malignant neoplasm of lung Associations of SNPs in LOC123688 (rs10519203; odds ratio [OR] = 1.60, 95% confi... BeFree 20554942 Detail
0.010 Carcinoma of lung We also investigated the relationship between the rs1051730 SNP in an intron of ... BeFree 21645942 Detail
<0.001 Malignant neoplasm of lung In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we ... BeFree 19247474 Detail
0.133 nicotine dependence Genotypes for two SNPs in the CHRNA3/5 region (rs8034191, rs1051730) previously ... BeFree 21232152 Detail
<0.001 Non-small cell lung cancer metastatic CHRNA3 (rs1051730) genotyping can improve customized chemotherapy based on tumor... BeFree 19733931 Detail
<0.001 Airway Obstruction Our findings suggest that rs1051730 in CHRNA is a susceptibility variant for COP... BeFree 22176972 Detail
<0.001 Drug habituation We, therefore, investigated the impact of two common CHRNA3 polymorphisms (rs105... BeFree 20393456 Detail
0.002 Carcinoma of lung Associations of SNPs in LOC123688 (rs10519203; odds ratio [OR] = 1.60, 95% confi... BeFree 20554942 Detail
0.010 Carcinoma of lung In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we ... BeFree 19247474 Detail
0.179 Malignant neoplasm of lung In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we ... BeFree 19247474 Detail
0.003 Adenocarcinoma of lung (disorder) [a lung cancer GWAS identified a distinct hereditary contribution to adenocarcin... GAD 19836008 Detail
0.060 Malignant neoplasm of lung In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we ... BeFree 19247474 Detail
0.005 nicotine dependence Cigarette consumption (P &lt; .001) and nicotine dependence (P = .036) were the ... BeFree 21747048 Detail
0.135 Lung Neoplasms [, a lung cancer GWAS identified a distinct hereditary contribution to adenocarc... GAD 19836008 Detail
0.179 Malignant neoplasm of lung Similarly, neither CHRNA3 rs8034191 nor rs1051730 were associated with lung canc... BeFree 20068085 Detail
0.179 Malignant neoplasm of lung Lung cancer susceptibility locus at 5p15.33. GWASCAT 18978790 Detail
0.020 nicotine dependence [A variant associated with nicotine dependence, lung cancer and peripheral arter... GAD 18385739 Detail
<0.001 Non-small cell lung cancer metastatic CHRNA3 (rs1051730) genotyping can improve customized chemotherapy based on tumor... BeFree 19733931 Detail
<0.001 cannabis abuse Rs16969968 in CHRNA5 (and its proxy, rs1051730 in CHRNA3) and rs1451240, a proxy... BeFree 25770649 Detail
0.134 Malignant neoplasm of lung Our findings demonstrated that CHRNA3 gene rs1051730-A allele and AGPHD1 gene rs... BeFree 22701590 Detail
0.133 nicotine dependence The CHRNA3 rs1051730 polymorphism has been associated to chronic obstructive pul... BeFree 22441734 Detail
0.179 Malignant neoplasm of lung Our findings demonstrated that CHRNA3 gene rs1051730-A allele and AGPHD1 gene rs... BeFree 22701590 Detail
0.133 nicotine dependence A recent genome-wide association study demonstrated an association between a com... BeFree 19429911 Detail
<0.001 Carcinoma of lung In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we ... BeFree 19247474 Detail
0.135 Lung Neoplasms [Lung cancer susceptibility locus at 5p15.33.] GAD 18978790 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000743.5(CHRNA3):c.645C>T (p.Tyr215=) AND Lung cancer susceptibility 2 ClinVar Detail
NM_000743.5(CHRNA3):c.645C>T (p.Tyr215=) AND Smoking as a quantitative trait locus 3 ClinVar Detail
NM_000743.5(CHRNA3):c.645C>T (p.Tyr215=) AND not provided ClinVar Detail
Associations of SNPs in LOC123688 (rs10519203; odds ratio [OR] = 1.60, 95% confidence interval [CI] ... DisGeNET Detail
In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we identified multiple ... DisGeNET Detail
We assessed the effect of nicotine on PPI, startle reactivity, and habituation in 52 healthy nonsmok... DisGeNET Detail
Rs16969968 in CHRNA5 (and its proxy, rs1051730 in CHRNA3) and rs1451240, a proxy for rs13280604 in C... DisGeNET Detail
NA DisGeNET Detail
Our findings demonstrated that CHRNA3 gene rs1051730-A allele and AGPHD1 gene rs8034191-T allele mig... DisGeNET Detail
In ever-smokers, the CHRNA3 rs1051730 genotype associated with reduced lung function and increased C... DisGeNET Detail
Associations of SNPs in LOC123688 (rs10519203; odds ratio [OR] = 1.60, 95% confidence interval [CI] ... DisGeNET Detail
In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we identified multiple ... DisGeNET Detail
Moreover, the TT genotype of the nicotinic acetylcholine receptor (nAChR) α3-subunit (CHRNA3) rs1051... DisGeNET Detail
In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we identified multiple ... DisGeNET Detail
A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. DisGeNET Detail
NA DisGeNET Detail
We also investigated the relationship between the rs1051730 SNP in an intron of the CHRNA3 gene (the... DisGeNET Detail
A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated wit... DisGeNET Detail
A genetic variant within the CHRNA5-CHRNA3-CHRNB4 region (rs1051730), previously associated with smo... DisGeNET Detail
[a lung cancer GWAS identified a distinct hereditary contribution to adenocarcinoma.] DisGeNET Detail
Our findings demonstrated that CHRNA3 gene rs1051730-A allele and AGPHD1 gene rs8034191-T allele mig... DisGeNET Detail
Similarly, neither CHRNA3 rs8034191 nor rs1051730 were associated with lung cancer risk. DisGeNET Detail
[A variant associated with nicotine dependence, lung cancer and peripheral arterial disease.] DisGeNET Detail
[A variant associated with nicotine dependence, lung cancer and peripheral arterial disease.] DisGeNET Detail
A recent genome-wide association study demonstrated an association between a common polymorphism (rs... DisGeNET Detail
Our findings suggest that rs1051730 in CHRNA is a susceptibility variant for COPD, in terms of both ... DisGeNET Detail
Association between CHRNA3 rs1051730 genotype and lung cancer risk in Chinese Han population: a case... DisGeNET Detail
In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we identified multiple ... DisGeNET Detail
Rs16969968 in CHRNA5 (and its proxy, rs1051730 in CHRNA3) and rs1451240, a proxy for rs13280604 in C... DisGeNET Detail
Association between CHRNA3 rs1051730 genotype and lung cancer risk in Chinese Han population: a case... DisGeNET Detail
A recent genome-wide association study demonstrated an association between a common polymorphism (rs... DisGeNET Detail
Associations of SNPs in LOC123688 (rs10519203; odds ratio [OR] = 1.60, 95% confidence interval [CI] ... DisGeNET Detail
We also investigated the relationship between the rs1051730 SNP in an intron of the CHRNA3 gene (the... DisGeNET Detail
In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we identified multiple ... DisGeNET Detail
Genotypes for two SNPs in the CHRNA3/5 region (rs8034191, rs1051730) previously associated with nico... DisGeNET Detail
CHRNA3 (rs1051730) genotyping can improve customized chemotherapy based on tumor assessment of ERCC1... DisGeNET Detail
Our findings suggest that rs1051730 in CHRNA is a susceptibility variant for COPD, in terms of both ... DisGeNET Detail
We, therefore, investigated the impact of two common CHRNA3 polymorphisms (rs1051730/rs1317286) on P... DisGeNET Detail
Associations of SNPs in LOC123688 (rs10519203; odds ratio [OR] = 1.60, 95% confidence interval [CI] ... DisGeNET Detail
In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we identified multiple ... DisGeNET Detail
In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we identified multiple ... DisGeNET Detail
[a lung cancer GWAS identified a distinct hereditary contribution to adenocarcinoma.] DisGeNET Detail
In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we identified multiple ... DisGeNET Detail
Cigarette consumption (P &lt; .001) and nicotine dependence (P = .036) were the highest in the combi... DisGeNET Detail
[, a lung cancer GWAS identified a distinct hereditary contribution to adenocarcinoma.] DisGeNET Detail
Similarly, neither CHRNA3 rs8034191 nor rs1051730 were associated with lung cancer risk. DisGeNET Detail
Lung cancer susceptibility locus at 5p15.33. DisGeNET Detail
[A variant associated with nicotine dependence, lung cancer and peripheral arterial disease.] DisGeNET Detail
CHRNA3 (rs1051730) genotyping can improve customized chemotherapy based on tumor assessment of ERCC1... DisGeNET Detail
Rs16969968 in CHRNA5 (and its proxy, rs1051730 in CHRNA3) and rs1451240, a proxy for rs13280604 in C... DisGeNET Detail
Our findings demonstrated that CHRNA3 gene rs1051730-A allele and AGPHD1 gene rs8034191-T allele mig... DisGeNET Detail
The CHRNA3 rs1051730 polymorphism has been associated to chronic obstructive pulmonary disease (COPD... DisGeNET Detail
Our findings demonstrated that CHRNA3 gene rs1051730-A allele and AGPHD1 gene rs8034191-T allele mig... DisGeNET Detail
A recent genome-wide association study demonstrated an association between a common polymorphism (rs... DisGeNET Detail
In the chr15q25.1 region spanning the nicotinic receptors CHRNA3 and CHRNA5, we identified multiple ... DisGeNET Detail
[Lung cancer susceptibility locus at 5p15.33.] 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
rs1051730 dbSNP
Genome
hg38
Position
chr15:78,601,997-78,601,997
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
98.58
Standard deviation of sample read depth (HGVD)
41.13
Number of reference allele (HGVD)
2371
Number of alternative allele (HGVD)
47
Allele Frequency (HGVD)
0.01943755169561621
Gene Symbol (HGVD)
CHRNA3
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))
rs1051730
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.021
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
352
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
269
East Asian Heterozygous Counts (ExAC)
261
East Asian Homozygous Counts (ExAC)
4
East Asian Allele Frequency (ExAC)
0.031098265895953756
Chromosome Counts in All Race (ExAC)
121262
Allele Counts in All Race (ExAC)
33101
Heterozygous Counts in All Race (ExAC)
22385
Homozygous Counts in All Race (ExAC)
5358
Allele Frequency in All Race (ExAC)
0.2729709224654055
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