chr5:176887433:C>T Detail (hg38) (HK3)

Information

Genome

Assembly Position
hg19 chr5:176,314,434-176,314,434 View the variant detail on this assembly version.
hg38 chr5:176,887,433-176,887,433

HGVS

Type Transcript Protein
RefSeq NM_002115.2:c.1600+18G>A
Ensemble ENST00000292432.10:c.1600+18G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.349
ToMMo:0.323
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.392

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 142570 OMIM
HGNC 4925 HGNC
Ensembl ENSG00000160883 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv23860795 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 premature menopause To identify whether variants found in a large Han Chinese cohort - 8q22.3 SNPs r... BeFree 24103315 Detail
0.002 premature menopause To identify whether variants found in a large Han Chinese cohort - 8q22.3 SNPs r... BeFree 24103315 Detail
Annotation

Annotations

DescrptionSourceLinks
To identify whether variants found in a large Han Chinese cohort - 8q22.3 SNPs rs3847153 and rs31089... DisGeNET Detail
To identify whether variants found in a large Han Chinese cohort - 8q22.3 SNPs rs3847153 and rs31089... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg38
Position
chr5:176,887,433-176,887,433
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
834
Mean of sample read depth (HGVD)
48.19
Standard deviation of sample read depth (HGVD)
21.96
Number of reference allele (HGVD)
1086
Number of alternative allele (HGVD)
582
Allele Frequency (HGVD)
0.3489208633093525
Gene Symbol (HGVD)
HK3
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))
rs2278493
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3227
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5408
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8568
East Asian Allele Counts (ExAC)
3357
East Asian Heterozygous Counts (ExAC)
2117
East Asian Homozygous Counts (ExAC)
620
East Asian Allele Frequency (ExAC)
0.3918067226890756
Chromosome Counts in All Race (ExAC)
119750
Allele Counts in All Race (ExAC)
41752
Heterozygous Counts in All Race (ExAC)
25996
Homozygous Counts in All Race (ExAC)
7878
Allele Frequency in All Race (ExAC)
0.3486597077244259
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