chr17:30204775:C>T Detail (hg38) (SLC6A4)

Information

Genome

Assembly Position
hg19 chr17:28,531,793-28,531,793 View the variant detail on this assembly version.
hg38 chr17:30,204,775-30,204,775

HGVS

Type Transcript Protein
RefSeq NM_001045.5:c.1651-1436G>A
Ensemble ENST00000261707.7:c.1651-1436G>A
ENST00000401766.6:c.1651-1436G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.826
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 182138 OMIM
HGNC 11050 HGNC
Ensembl ENSG00000108576 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57464736 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.188 Mood Disorders Three genes contributed exclusively to mood disorders, one through a main effect... BeFree 19381154 Detail
0.018 Mood Disorders Three genes contributed exclusively to mood disorders, one through a main effect... BeFree 19381154 Detail
0.155 Mental Depression The major allele of another SNP of SLC6A4, namely rs3794808, correlated with the... BeFree 20981038 Detail
0.282 depressive disorder The major allele of another SNP of SLC6A4, namely rs3794808, correlated with the... BeFree 20981038 Detail
Annotation

Annotations

DescrptionSourceLinks
Three genes contributed exclusively to mood disorders, one through a main effect (HTR5A (rs1657268))... DisGeNET Detail
Three genes contributed exclusively to mood disorders, one through a main effect (HTR5A (rs1657268))... DisGeNET Detail
The major allele of another SNP of SLC6A4, namely rs3794808, correlated with the HADS depression sco... DisGeNET Detail
The major allele of another SNP of SLC6A4, namely rs3794808, correlated with the HADS depression sco... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs3794808 dbSNP
Genome
hg38
Position
chr17:30,204,775-30,204,775
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs3794808
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8263
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
13849
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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