chr6:31783863:G>C Detail (hg19) (HSPA1A)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:31,783,863-31,783,863 |
| hg38 | chr6:31,816,086-31,816,086 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_005345.5:c.330G>C | NP_005336.3:p.Glu110Asp |
| Ensemble | ENST00000608703.1:c.76-241G>C | |
| ENST00000375651.7:c.330G>C | ENST00000375651.7:p.Glu110Asp |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | |
| GWAS entry | 1 |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.074 |
| ToMMo:0.054 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.250 |
Prediction
ClinVar
| Clinical Significance |
association
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
not provided
|
biliary cirrhosis, primary |
not provided
|
MGS000089
(TMGS000168) |
Minoru Nakamura Minoru Nakamura |
National Hospital Organization Nagasaki Medical Center National Hospital Organization Nagasaki Medical Center |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
association
|
2019-08-04 | no assertion criteria provided | chronic obstructive pulmonary disease |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.006 | bipolar disorder | We have further studied a previously investigated sample of 187 major depressive... | BeFree | 19582769 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_005345.6(HSPA1A):c.330G>C (p.Glu110Asp) AND Chronic obstructive pulmonary disease | ClinVar | Detail |
| We have further studied a previously investigated sample of 187 major depressive disorder (MDD) pati... | 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
- rs562047 dbSNP
- Genome
- hg19
- Position
- chr6:31,783,863-31,783,863
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- C
- Filtering Status (HGVD)
- VQSRTrancheSNP99.00to99.90
- # of samples (HGVD)
- 102
- Mean of sample read depth (HGVD)
- 24.83
- Standard deviation of sample read depth (HGVD)
- 50.75
- Number of reference allele (HGVD)
- 189
- Number of alternative allele (HGVD)
- 15
- Allele Frequency (HGVD)
- 0.07352941176470588
- Gene Symbol (HGVD)
- HSPA1A
- 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))
- rs562047
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0536
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 879
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16412
- East Asian Chromosome Counts (ExAC)
- 32
- East Asian Allele Counts (ExAC)
- 8
- East Asian Heterozygous Counts (ExAC)
- 2
- East Asian Homozygous Counts (ExAC)
- 3
- East Asian Allele Frequency (ExAC)
- 0.25
- Chromosome Counts in All Race (ExAC)
- 350
- Allele Counts in All Race (ExAC)
- 90
- Heterozygous Counts in All Race (ExAC)
- 64
- Homozygous Counts in All Race (ExAC)
- 13
- Allele Frequency in All Race (ExAC)
- 0.2571428571428571
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