chr4:37962186:G>C Detail (hg19) (PTTG2, TBC1D1)

Information

Genome

Assembly Position
hg19 chr4:37,962,186-37,962,186
hg38 chr4:37,960,565-37,960,565 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_006607.2:c.131G>C NP_006598.2:p.Arg44Pro
Ensemble ENST00000504686.2:c.131G>C ENST00000504686.2:p.Arg44Pro
Type Transcript Protein
RefSeq NM_015173.3:c.418-53944G>C
NM_001253912.1:c.418-53944G>C
Ensemble ENST00000261439.9:c.418-53944G>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.961
ToMMo:0.964
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.957

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 604231 OMIM
HGNC 9691 HGNC
Ensembl ENSG00000250254 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv16699930 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 609850 OMIM
HGNC 11578 HGNC
Ensembl ENSG00000065882 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv16699930 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
<0.001 Completed Suicide The nonsynonymous variants rs1383180 in EVC gene, rs6811863 in TBC1D1 gene, rs36... BeFree 19115052 Detail
<0.001 Completed Suicide The nonsynonymous variants rs1383180 in EVC gene, rs6811863 in TBC1D1 gene, rs36... BeFree 19115052 Detail
<0.001 Completed Suicide The nonsynonymous variants rs1383180 in EVC gene, rs6811863 in TBC1D1 gene, rs36... BeFree 19115052 Detail
Annotation

Annotations

DescrptionSourceLinks
The nonsynonymous variants rs1383180 in EVC gene, rs6811863 in TBC1D1 gene, rs362272 in HTT gene, an... DisGeNET Detail
The nonsynonymous variants rs1383180 in EVC gene, rs6811863 in TBC1D1 gene, rs362272 in HTT gene, an... DisGeNET Detail
The nonsynonymous variants rs1383180 in EVC gene, rs6811863 in TBC1D1 gene, rs362272 in HTT gene, an... 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
-
Genome
hg19
Position
chr4:37,962,186-37,962,186
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
94.55
Standard deviation of sample read depth (HGVD)
41.67
Number of reference allele (HGVD)
93
Number of alternative allele (HGVD)
2321
Allele Frequency (HGVD)
0.9614747307373653
Gene Symbol (HGVD)
PTTG2
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))
rs6811863
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9643
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16161
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
8282
East Asian Heterozygous Counts (ExAC)
358
East Asian Homozygous Counts (ExAC)
3962
East Asian Allele Frequency (ExAC)
0.9572353213129912
Chromosome Counts in All Race (ExAC)
121036
Allele Counts in All Race (ExAC)
77621
Heterozygous Counts in All Race (ExAC)
26107
Homozygous Counts in All Race (ExAC)
25757
Allele Frequency in All Race (ExAC)
0.6413050662612776
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