chr12:72425954:G>A Detail (hg19) (TPH2)

Information

Genome

Assembly Position
hg19 chr12:72,425,954-72,425,954
hg38 chr12:72,032,174-72,032,174 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_173353.3:c.*479G>A
Ensemble ENST00000333850.4:c.*479G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.245
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 607478 OMIM
HGNC 20692 HGNC
Ensembl ENSG00000139287 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv46390992 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-01-13 criteria provided, single submitter Tryptophan 5-monooxygenase deficiency germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Psychotic Disorders More specifically, we observed that the T allele in the rs4570625 polymorphism w... BeFree 24491795 Detail
<0.001 Alcohol abuse More specifically, we observed that the T allele in the rs4570625 polymorphism w... BeFree 24491795 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_173353.4(TPH2):c.*479G>A AND Tryptophan 5-monooxygenase deficiency ClinVar Detail
More specifically, we observed that the T allele in the rs4570625 polymorphism was associated with p... DisGeNET Detail
More specifically, we observed that the T allele in the rs4570625 polymorphism was associated with p... 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
rs17110747 dbSNP
Genome
hg19
Position
chr12:72,425,954-72,425,954
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs17110747
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2446
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4100
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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