chr4:3234980:G>A Detail (hg19) (HTT)

Information

Genome

Assembly Position
hg19 chr4:3,234,980-3,234,980
hg38 chr4:3,233,253-3,233,253 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002111.7:c.8356G>A NP_002102.4:p.Val2786Ile
Ensemble ENST00000355072.11:c.8356G>A ENST00000355072.11:p.Val2786Ile
ENST00000680956.1:c.8098G>A ENST00000680956.1:p.Val2700Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.341
ToMMo:0.332
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.360

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 613004 OMIM
HGNC 4851 HGNC
Ensembl ENSG00000197386 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv15860896 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-29 criteria provided, single submitter not provided germline Detail
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
NM_001388492.1(HTT):c.8356G>A (p.Val2786Ile) AND not provided ClinVar 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
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
-
dbSNP
rs362272 dbSNP
Genome
hg19
Position
chr4:3,234,980-3,234,980
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1206
Mean of sample read depth (HGVD)
57.10
Standard deviation of sample read depth (HGVD)
32.51
Number of reference allele (HGVD)
1590
Number of alternative allele (HGVD)
822
Allele Frequency (HGVD)
0.3407960199004975
Gene Symbol (HGVD)
HTT
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))
rs362272
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.332
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5564
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Homozygous Counts in All Race (ExAC)
5255
East Asian Chromosome Counts (ExAC)
8560
East Asian Allele Counts (ExAC)
3081
East Asian Heterozygous Counts (ExAC)
1983
East Asian Homozygous Counts (ExAC)
549
East Asian Allele Frequency (ExAC)
0.3599299065420561
Chromosome Counts in All Race (ExAC)
120100
Allele Counts in All Race (ExAC)
33689
Heterozygous Counts in All Race (ExAC)
23178
Allele Frequency in All Race (ExAC)
0.2805079100749375
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