chr6:32029226:A>G Detail (hg19) (TNXB)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:32,029,226-32,029,226 |
| hg38 | chr6:32,061,449-32,061,449 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_019105.6:c.7440T>C | NP_061978.6:p.Tyr2480= |
| Ensemble | ENST00000375244.7:c.7440T>C | ENST00000375244.7:p.Tyr2480= |
| ENST00000644971.2:c.7440T>C | ENST00000644971.2:p.Tyr2480= |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | |
| GWAS entry | 1 |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.659 |
| ToMMo:0.706 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.627 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| 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 |
|---|---|---|---|---|---|
|
Benign
|
criteria provided, single submitter | not specified |
germline
|
Detail | |
|
Benign
|
2018-09-19 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2021-09-10 | criteria provided, single submitter | Ehlers-Danlos syndrome due to tenascin-X deficiency |
germline
|
Detail |
|
Benign
|
2021-09-10 | criteria provided, single submitter | Vesicoureteral reflux 8 |
germline
|
Detail |
|
Benign
|
2018-12-04 | criteria provided, single submitter |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.004 | schizophrenia | The TDT analysis demonstrated that of the nine SNPs, three were associated with ... | BeFree | 14755442 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001365276.2(TNXB):c.7440T>C (p.Tyr2480=) AND not specified | ClinVar | Detail |
| NM_001365276.2(TNXB):c.7440T>C (p.Tyr2480=) AND not provided | ClinVar | Detail |
| NM_001365276.2(TNXB):c.7440T>C (p.Tyr2480=) AND Ehlers-Danlos syndrome due to tenascin-X deficiency | ClinVar | Detail |
| NM_001365276.2(TNXB):c.7440T>C (p.Tyr2480=) AND Vesicoureteral reflux 8 | ClinVar | Detail |
| NM_001365276.2(TNXB):c.7440T>C (p.Tyr2480=) AND Cardiovascular phenotype | ClinVar | Detail |
| The TDT analysis demonstrated that of the nine SNPs, three were associated with schizophrenia, inclu... | 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
- rs204887 dbSNP
- Genome
- hg19
- Position
- chr6:32,029,226-32,029,226
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- VQSRTrancheSNP99.00to99.90
- # of samples (HGVD)
- 1085
- Mean of sample read depth (HGVD)
- 50.00
- Standard deviation of sample read depth (HGVD)
- 24.62
- Number of reference allele (HGVD)
- 740
- Number of alternative allele (HGVD)
- 1430
- Allele Frequency (HGVD)
- 0.6589861751152074
- Gene Symbol (HGVD)
- TNXB
- 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))
- rs204887
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.7061
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 11832
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16758
- East Asian Chromosome Counts (ExAC)
- 8580
- East Asian Allele Counts (ExAC)
- 5376
- East Asian Heterozygous Counts (ExAC)
- 1976
- East Asian Homozygous Counts (ExAC)
- 1700
- East Asian Allele Frequency (ExAC)
- 0.6265734265734266
- Chromosome Counts in All Race (ExAC)
- 118400
- Allele Counts in All Race (ExAC)
- 81776
- Heterozygous Counts in All Race (ExAC)
- 24534
- Homozygous Counts in All Race (ExAC)
- 28621
- Allele Frequency in All Race (ExAC)
- 0.6906756756756757
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