chr15:78618839:T>C Detail (hg38) (CHRNA3)

Information

Genome

Assembly Position
hg19 chr15:78,911,181-78,911,181 View the variant detail on this assembly version.
hg38 chr15:78,618,839-78,618,839

HGVS

Type Transcript Protein
RefSeq NM_000743.4:c.159A>G NP_000734.2:p.Val53=
NM_001166694.1:c.159A>G NP_001160166.1:p.Val53=
Ensemble ENST00000326828.6:c.159A>G ENST00000326828.6:p.Val53=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.340
ToMMo:0.347
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.363

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 tgv53653826 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-07-22 criteria provided, single submitter Urinary bladder, atony of 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
<0.001 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
0.120 Pulmonary function (finding) Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies... GWASCAT 23284291 Detail
0.121 obesity Identified genome-wide significant loci: 1) corroborated genes implicated in oth... GWASCAT 23251661 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000743.5(CHRNA3):c.159A>G (p.Val53=) AND Urinary bladder, atony of ClinVar Detail
NM_000743.5(CHRNA3):c.159A>G (p.Val53=) AND not provided ClinVar 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
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulm... DisGeNET Detail
Identified genome-wide significant loci: 1) corroborated genes implicated in other studies (MTNR1B, ... 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
rs8040868 dbSNP
Genome
hg38
Position
chr15:78,618,839-78,618,839
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1205
Mean of sample read depth (HGVD)
78.20
Standard deviation of sample read depth (HGVD)
37.59
Number of reference allele (HGVD)
1589
Number of alternative allele (HGVD)
820
Allele Frequency (HGVD)
0.340390203403902
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))
rs8040868
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3468
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5813
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8628
East Asian Allele Counts (ExAC)
3136
East Asian Heterozygous Counts (ExAC)
1992
East Asian Homozygous Counts (ExAC)
572
East Asian Allele Frequency (ExAC)
0.36346777932313395
Chromosome Counts in All Race (ExAC)
121276
Allele Counts in All Race (ExAC)
43447
Heterozygous Counts in All Race (ExAC)
27035
Homozygous Counts in All Race (ExAC)
8206
Allele Frequency in All Race (ExAC)
0.3582489528018734
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