chr12:71979082:A>G Detail (hg38) (TPH2)

Information

Genome

Assembly Position
hg19 chr12:72,372,862-72,372,862 View the variant detail on this assembly version.
hg38 chr12:71,979,082-71,979,082

HGVS

Type Transcript Protein
RefSeq NM_173353.3:c.936A>G NP_775489.2:p.Pro312=
Ensemble ENST00000333850.4:c.936A>G ENST00000333850.4:p.Pro312=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.560
ToMMo:0.550
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.475

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 607478 OMIM
HGNC 20692 HGNC
Ensembl ENSG00000139287 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv46389802 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-03-06 criteria provided, single submitter Tryptophan 5-monooxygenase deficiency germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.127 depressive disorder We hypothesize that functional polymorphisms (TPH2: rs7305115, 5-HTTLPR and rs25... BeFree 25214390 Detail
0.282 depressive disorder We hypothesize that functional polymorphisms (TPH2: rs7305115, 5-HTTLPR and rs25... BeFree 25214390 Detail
0.007 Unipolar Depression Effect of tryptophan hydroxylase-2 rs7305115 SNP on suicide attempts risk in maj... BeFree 20738857 Detail
0.028 Mental Depression [The study suggested that hopelessness, negative life events and family history ... GAD 20738857 Detail
0.211 major depressive disorder Effect of tryptophan hydroxylase-2 rs7305115 SNP on suicide attempts risk in maj... BeFree 20738857 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_173353.4(TPH2):c.936A>G (p.Pro312=) AND Tryptophan 5-monooxygenase deficiency ClinVar Detail
We hypothesize that functional polymorphisms (TPH2: rs7305115, 5-HTTLPR and rs25531) within both gen... DisGeNET Detail
We hypothesize that functional polymorphisms (TPH2: rs7305115, 5-HTTLPR and rs25531) within both gen... DisGeNET Detail
Effect of tryptophan hydroxylase-2 rs7305115 SNP on suicide attempts risk in major depression. DisGeNET Detail
[The study suggested that hopelessness, negative life events and family history of suicide were risk... DisGeNET Detail
Effect of tryptophan hydroxylase-2 rs7305115 SNP on suicide attempts risk in major depression. 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
rs7305115 dbSNP
Genome
hg38
Position
chr12:71,979,082-71,979,082
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1064
Mean of sample read depth (HGVD)
32.55
Standard deviation of sample read depth (HGVD)
38.22
Number of reference allele (HGVD)
936
Number of alternative allele (HGVD)
1192
Allele Frequency (HGVD)
0.5601503759398496
Gene Symbol (HGVD)
TPH2
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))
rs7305115
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5496
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9211
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)
4107
East Asian Heterozygous Counts (ExAC)
2183
East Asian Homozygous Counts (ExAC)
962
East Asian Allele Frequency (ExAC)
0.4751272559000463
Chromosome Counts in All Race (ExAC)
121376
Allele Counts in All Race (ExAC)
68536
Heterozygous Counts in All Race (ExAC)
29468
Homozygous Counts in All Race (ExAC)
19534
Allele Frequency in All Race (ExAC)
0.5646585815976799
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