chr15:78917399:A>G Detail (hg19) (CHRNB4)

Information

Genome

Assembly Position
hg19 chr15:78,917,399-78,917,399
hg38 chr15:78,625,057-78,625,057 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001256567.1:c.594T>C NP_001243496.1:p.Ala198=
NM_000750.3:c.*76T>C
Ensemble ENST00000412074.6:c.594T>C ENST00000412074.6:p.Ala198=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.604
ToMMo:0.599
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.529

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 118509 OMIM
HGNC 1964 HGNC
Ensembl ENSG00000117971 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv53654064 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2020-04-27 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
Annotation

Annotations

DescrptionSourceLinks
NM_000750.5(CHRNB4):c.*76T>C 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

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
rs1948 dbSNP
Genome
hg19
Position
chr15:78,917,399-78,917,399
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1182
Mean of sample read depth (HGVD)
39.18
Standard deviation of sample read depth (HGVD)
22.08
Number of reference allele (HGVD)
936
Number of alternative allele (HGVD)
1425
Allele Frequency (HGVD)
0.6035578144853876
Gene Symbol (HGVD)
CHRNB4
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))
rs1948
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5991
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10041
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8492
East Asian Allele Counts (ExAC)
4492
East Asian Heterozygous Counts (ExAC)
2108
East Asian Homozygous Counts (ExAC)
1192
East Asian Allele Frequency (ExAC)
0.5289684408855393
Chromosome Counts in All Race (ExAC)
119328
Allele Counts in All Race (ExAC)
82457
Heterozygous Counts in All Race (ExAC)
24709
Homozygous Counts in All Race (ExAC)
28874
Allele Frequency in All Race (ExAC)
0.6910113301153125
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