chr15:78590583:G>A Detail (hg38) (CHRNA5)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr15:78,882,925-78,882,925 View the variant detail on this assembly version. |
| hg38 | chr15:78,590,583-78,590,583 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000745.3:c.1192G>A | NP_000736.2:p.Asp398Asn |
| NM_001307945.1:c.458+734G>A | ||
| Ensemble | ENST00000299565.9:c.1192G>A | ENST00000299565.9:p.Asp398Asn |
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:0.030 |
Prediction
ClinVar
| Clinical Significance |
drug response
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
risk factor
|
2010-07-27 | no assertion criteria provided | Lung cancer susceptibility 2 |
germline
|
Detail |
|
risk factor
|
2010-07-27 | no assertion criteria provided | Smoking as a quantitative trait locus 3 |
germline
|
Detail |
|
drug response
|
2021-03-24 | reviewed by expert panel |
germline
|
Detail | |
Uncertain significance
|
no assertion criteria provided | Susceptibility to severe coronavirus disease (COVID-19) due to high levels of fibrinogen and C-reactive protein |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.012 | Carcinoma of lung | A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) ... | BeFree | 20587604 | Detail |
| 0.179 | Malignant neoplasm of lung | A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) ... | BeFree | 20587604 | Detail |
| 0.060 | Malignant neoplasm of lung | A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) ... | BeFree | 20587604 | Detail |
| 0.010 | Carcinoma of lung | A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) ... | BeFree | 20587604 | Detail |
| <0.001 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| 0.133 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| <0.001 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| <0.001 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| 0.020 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| <0.001 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| 0.133 | nicotine dependence | Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968... | BeFree | 20840187 | Detail |
| 0.006 | nicotine dependence | Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968... | BeFree | 20840187 | Detail |
| <0.001 | nicotine dependence | Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968... | BeFree | 20840187 | Detail |
| 0.133 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.012 | Carcinoma of lung | Sliding window haplotype analysis within chromosome 15, evaluating 4722250 haplo... | BeFree | 26282330 | Detail |
| <0.001 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.020 | nicotine dependence | Minor allele carriers at rs16969968 in the nicotinic acetylcholine receptor α5 s... | BeFree | 24934182 | Detail |
| 0.020 | nicotine dependence | Our study showed a low to moderate level of ND in the Kashubians, influenced by ... | BeFree | 25652844 | Detail |
| 0.120 | LUNG CANCER SUSCEPTIBILITY 2 (disorder) | NA | CLINVAR | Detail | |
| 0.020 | nicotine dependence | Recently a candidate gene study in nicotine dependent cases and nondependent smo... | BeFree | 18414406 | Detail |
| 0.003 | Adenocarcinoma of lung (disorder) | The carrier status of the 398N allele at the D398N polymorphism of the CHRNA5 ge... | BeFree | 19223495 | Detail |
| 0.060 | Malignant neoplasm of lung | Sliding window haplotype analysis within chromosome 15, evaluating 4722250 haplo... | BeFree | 26282330 | Detail |
| 0.020 | nicotine dependence | Peer smoking had a substantially lower effect on nicotine dependence among those... | BeFree | 20840187 | Detail |
| 0.020 | nicotine dependence | Genome wide association studies revealed a relationship between development of n... | BeFree | 21764527 | Detail |
| 0.060 | Malignant neoplasm of lung | No association with lung cancer risk was found for CHRNA5 rs16969968. | BeFree | 23178447 | Detail |
| 0.020 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.060 | Malignant neoplasm of lung | Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CH... | BeFree | 21862624 | Detail |
| 0.010 | Carcinoma of lung | Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CH... | BeFree | 21862624 | Detail |
| 0.012 | Carcinoma of lung | No association with lung cancer risk was found for CHRNA5 rs16969968. | BeFree | 23178447 | Detail |
| 0.003 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.133 | Alcoholic Intoxication, Chronic | The analysis revealed a candidate SNP from CHRNA5, rs16969968, associated with b... | BeFree | 23334941 | Detail |
| 0.003 | Adenocarcinoma of lung (disorder) | CHRNA5 gene D398N polymorphism in Japanese lung adenocarcinoma. | BeFree | 19577767 | Detail |
| 0.002 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.007 | adenocarcinoma | In addition, the same D398N variation correlated with CHRNA5 mRNA levels in norm... | BeFree | 19223495 | Detail |
| 0.120 | SMOKING AS A QUANTITATIVE TRAIT LOCUS 3 (disorder) | NA | CLINVAR | Detail | |
| 0.133 | nicotine dependence | Recently a candidate gene study in nicotine dependent cases and nondependent smo... | BeFree | 18414406 | Detail |
| 0.020 | nicotine dependence | The analysis revealed a candidate SNP from CHRNA5, rs16969968, associated with b... | BeFree | 23334941 | Detail |
| 0.012 | Carcinoma of lung | Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CH... | BeFree | 21862624 | Detail |
| 0.179 | Malignant neoplasm of lung | Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CH... | BeFree | 21862624 | Detail |
| 0.001 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.020 | nicotine dependence | One CHRNA5 (rs16969968) and two CHRNA3 (rs1051703, rs6495308) SNPs were examined... | BeFree | 22223462 | Detail |
| 0.133 | nicotine dependence | One CHRNA5 (rs16969968) and two CHRNA3 (rs1051703, rs6495308) SNPs were examined... | BeFree | 22223462 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000745.4(CHRNA5):c.1192G>A (p.Asp398Asn) AND Lung cancer susceptibility 2 | ClinVar | Detail |
| NM_000745.4(CHRNA5):c.1192G>A (p.Asp398Asn) AND Smoking as a quantitative trait locus 3 | ClinVar | Detail |
| NM_000745.4(CHRNA5):c.1192G>A (p.Asp398Asn) AND nicotine response - Toxicity | ClinVar | Detail |
| NM_000745.4(CHRNA5):c.1192G>A (p.Asp398Asn) AND Susceptibility to severe coronavirus disease (COVID-... | ClinVar | Detail |
| A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) and CHRNA3 (rs578776... | DisGeNET | Detail |
| A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) and CHRNA3 (rs578776... | DisGeNET | Detail |
| A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) and CHRNA3 (rs578776... | DisGeNET | Detail |
| A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) and CHRNA3 (rs578776... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968), CHRNA3 (rs578776)... | DisGeNET | Detail |
| Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968), CHRNA3 (rs578776)... | DisGeNET | Detail |
| Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968), CHRNA3 (rs578776)... | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| Sliding window haplotype analysis within chromosome 15, evaluating 4722250 haplotypes and pair-wise ... | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| Minor allele carriers at rs16969968 in the nicotinic acetylcholine receptor α5 subunit gene (CHRNA5)... | DisGeNET | Detail |
| Our study showed a low to moderate level of ND in the Kashubians, influenced by age, sex, as well as... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| Recently a candidate gene study in nicotine dependent cases and nondependent smoking controls report... | DisGeNET | Detail |
| The carrier status of the 398N allele at the D398N polymorphism of the CHRNA5 gene was associated wi... | DisGeNET | Detail |
| Sliding window haplotype analysis within chromosome 15, evaluating 4722250 haplotypes and pair-wise ... | DisGeNET | Detail |
| Peer smoking had a substantially lower effect on nicotine dependence among those with the high-risk ... | DisGeNET | Detail |
| Genome wide association studies revealed a relationship between development of nicotine dependence a... | DisGeNET | Detail |
| No association with lung cancer risk was found for CHRNA5 rs16969968. | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CHRNA3 on 15q25, rs169... | DisGeNET | Detail |
| Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CHRNA3 on 15q25, rs169... | DisGeNET | Detail |
| No association with lung cancer risk was found for CHRNA5 rs16969968. | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| The analysis revealed a candidate SNP from CHRNA5, rs16969968, associated with both ND and AD, and r... | DisGeNET | Detail |
| CHRNA5 gene D398N polymorphism in Japanese lung adenocarcinoma. | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| In addition, the same D398N variation correlated with CHRNA5 mRNA levels in normal lung of adenocarc... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| Recently a candidate gene study in nicotine dependent cases and nondependent smoking controls report... | DisGeNET | Detail |
| The analysis revealed a candidate SNP from CHRNA5, rs16969968, associated with both ND and AD, and r... | DisGeNET | Detail |
| Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CHRNA3 on 15q25, rs169... | DisGeNET | Detail |
| Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CHRNA3 on 15q25, rs169... | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| One CHRNA5 (rs16969968) and two CHRNA3 (rs1051703, rs6495308) SNPs were examined for their ability t... | DisGeNET | Detail |
| One CHRNA5 (rs16969968) and two CHRNA3 (rs1051703, rs6495308) SNPs were examined for their ability t... | 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
- rs16969968 dbSNP
- Genome
- hg38
- Position
- chr15:78,590,583-78,590,583
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 98.85
- Standard deviation of sample read depth (HGVD)
- 45.98
- Number of reference allele (HGVD)
- 2373
- Number of alternative allele (HGVD)
- 47
- Allele Frequency (HGVD)
- 0.019421487603305785
- Gene Symbol (HGVD)
- CHRNA5
- 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))
- rs16969968
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0207
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 347
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8644
- East Asian Allele Counts (ExAC)
- 260
- East Asian Heterozygous Counts (ExAC)
- 254
- East Asian Homozygous Counts (ExAC)
- 3
- East Asian Allele Frequency (ExAC)
- 0.03007866728366497
- Chromosome Counts in All Race (ExAC)
- 121044
- Allele Counts in All Race (ExAC)
- 32400
- Heterozygous Counts in All Race (ExAC)
- 21838
- Homozygous Counts in All Race (ExAC)
- 5281
- Allele Frequency in All Race (ExAC)
- 0.2676712600376723
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