chr6:32223953:G>A Detail (hg38) (NOTCH4)

Information

Genome

Assembly Position
hg19 chr6:32,191,730-32,191,730 View the variant detail on this assembly version.
hg38 chr6:32,223,953-32,223,953

HGVS

Type Transcript Protein
RefSeq NM_004557.3:c.-25C>T
NR_134949.1:c.-25C>T
NR_134950.1:c.-25C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.486
ToMMo:0.478
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.356

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 164951 OMIM
HGNC 7884 HGNC
Ensembl ENSG00000204301 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24821187 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 Invasive Ductal Breast Carcinoma A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... BeFree 25120811 Detail
<0.001 Noninfiltrating Intraductal Carcinoma A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... BeFree 25120811 Detail
<0.001 Noninfiltrating Intraductal Carcinoma A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... BeFree 25120811 Detail
<0.001 Noninfiltrating Intraductal Carcinoma A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... BeFree 25120811 Detail
<0.001 Invasive Ductal Breast Carcinoma A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... BeFree 25120811 Detail
<0.001 Invasive Ductal Breast Carcinoma A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (... BeFree 25120811 Detail
0.197 schizophrenia Methylation analysis of the NOTCH4 -25 C/T polymorphism in schizophrenia. BeFree 21085055 Detail
Annotation

Annotations

DescrptionSourceLinks
A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... DisGeNET Detail
A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... DisGeNET Detail
A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... DisGeNET Detail
A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... DisGeNET Detail
A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... DisGeNET Detail
A total of 100 invasive ductal carcinoma (IDC) and 50 ductal carcinoma in situ (DCIS) patients and 1... DisGeNET Detail
Methylation analysis of the NOTCH4 -25 C/T polymorphism in schizophrenia. 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
hg38
Position
chr6:32,223,953-32,223,953
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
772
Mean of sample read depth (HGVD)
24.80
Standard deviation of sample read depth (HGVD)
10.85
Number of reference allele (HGVD)
793
Number of alternative allele (HGVD)
751
Allele Frequency (HGVD)
0.48639896373056996
Gene Symbol (HGVD)
NOTCH4
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))
rs367398
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4779
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8008
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
East Asian Chromosome Counts (ExAC)
6716
East Asian Allele Counts (ExAC)
2389
East Asian Heterozygous Counts (ExAC)
1647
East Asian Homozygous Counts (ExAC)
371
East Asian Allele Frequency (ExAC)
0.35571768910065515
Chromosome Counts in All Race (ExAC)
96384
Allele Counts in All Race (ExAC)
36394
Heterozygous Counts in All Race (ExAC)
22810
Homozygous Counts in All Race (ExAC)
6792
Allele Frequency in All Race (ExAC)
0.377593791500664
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