chr15:78615690:A>G Detail (hg38) (CHRNA3)

Information

Genome

Assembly Position
hg19 chr15:78,908,032-78,908,032 View the variant detail on this assembly version.
hg38 chr15:78,615,690-78,615,690

HGVS

Type Transcript Protein
RefSeq NM_000743.4:c.377+1334T>C
NM_001166694.1:c.377+1334T>C
Ensemble ENST00000326828.6:c.377+1334T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.788
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

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 tgv53653617 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
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 Smoker's lung To examine if variation at any of these loci influences the risk of lung cancer ... BeFree 19955392 Detail
0.123 schizophrenia Biological insights from 108 schizophrenia-associated genetic loci. GWASCAT 25056061 Detail
0.135 Lung Neoplasms [Common 5p15.33 and 6p21.33 variants influence lung cancer risk.] GAD 18978787 Detail
0.179 Malignant neoplasm of lung Common 5p15.33 and 6p21.33 variants influence lung cancer risk. GWASCAT 18978787 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000743.5(CHRNA3):c.377+1334T>C AND not provided ClinVar Detail
To examine if variation at any of these loci influences the risk of lung cancer in never-smokers, we... DisGeNET Detail
Biological insights from 108 schizophrenia-associated genetic loci. DisGeNET Detail
[Common 5p15.33 and 6p21.33 variants influence lung cancer risk.] DisGeNET Detail
Common 5p15.33 and 6p21.33 variants influence lung cancer risk. DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg38
Position
chr15:78,615,690-78,615,690
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))
rs8042374
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7881
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
13208
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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