chr6:31572779:T>C Detail (hg38) (LTA)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:31,540,556-31,540,556 View the variant detail on this assembly version. |
| hg38 | chr6:31,572,779-31,572,779 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000595.3:c.37T>C | NP_000586.2:p.Cys13Arg |
| Ensemble | ENST00000418386.3:c.37T>C | ENST00000418386.3:p.Cys13Arg |
| ENST00000454783.5:c.37T>C | ENST00000454783.5:p.Cys13Arg |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.154 |
| ToMMo:0.187 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.198 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2019-10-17 | criteria provided, single submitter | LTA-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.008 | Behcet Syndrome | [Genome-wide association study identifies variants in the MHC class I, IL10, and... | GAD | 20622878 | Detail |
| 0.001 | Depressive Symptoms | Results from the recruited cohort (n = 190) indicated strong statistical evidenc... | BeFree | 24598699 | Detail |
| 0.009 | Fatigue | Evening fatigue was associated with caring for children at home and variations i... | BeFree | 24872120 | Detail |
| <0.001 | Shoulder Pain | Results from the recruited cohort (n = 190) indicated strong statistical evidenc... | BeFree | 24598699 | Detail |
| <0.001 | squamous cell carcinoma | Statistically significant risks were observed for HPV16-containing SCC of the ce... | BeFree | 26241630 | Detail |
| <0.001 | Fatigue | Evening fatigue was associated with caring for children at home and variations i... | BeFree | 24872120 | Detail |
| <0.001 | Depressive Symptoms | Results from the recruited cohort (n = 190) indicated strong statistical evidenc... | BeFree | 24598699 | Detail |
| 0.121 | Pain | Results from the recruited cohort (n = 190) indicated strong statistical evidenc... | BeFree | 24598699 | Detail |
| 0.001 | Pain | Results from the recruited cohort (n = 190) indicated strong statistical evidenc... | BeFree | 24598699 | Detail |
| <0.001 | Shoulder Pain | Results from the recruited cohort (n = 190) indicated strong statistical evidenc... | BeFree | 24598699 | Detail |
| 0.025 | squamous cell carcinoma | Statistically significant risks were observed for HPV16-containing SCC of the ce... | BeFree | 26241630 | Detail |
| 0.031 | Diabetes Mellitus, Non-Insulin-Dependent | Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs36152... | BeFree | 20177654 | Detail |
| 0.022 | Metabolic syndrome X | Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs36152... | BeFree | 20177654 | Detail |
| 0.008 | Cardiovascular Diseases | In this clinical study, the influence of genetic variants of TNF-beta (c.7G>A... | BeFree | 17194634 | Detail |
| 0.009 | Metabolic syndrome X | Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs36152... | BeFree | 20177654 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000595.4(LTA):c.37T>C (p.Cys13Arg) AND LTA-related disorder | ClinVar | Detail |
| [Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regio... | DisGeNET | Detail |
| Results from the recruited cohort (n = 190) indicated strong statistical evidence for the interactio... | DisGeNET | Detail |
| Evening fatigue was associated with caring for children at home and variations in interleukin 4 (IL4... | DisGeNET | Detail |
| Results from the recruited cohort (n = 190) indicated strong statistical evidence for the interactio... | DisGeNET | Detail |
| Statistically significant risks were observed for HPV16-containing SCC of the cervix with the varian... | DisGeNET | Detail |
| Evening fatigue was associated with caring for children at home and variations in interleukin 4 (IL4... | DisGeNET | Detail |
| Results from the recruited cohort (n = 190) indicated strong statistical evidence for the interactio... | DisGeNET | Detail |
| Results from the recruited cohort (n = 190) indicated strong statistical evidence for the interactio... | DisGeNET | Detail |
| Results from the recruited cohort (n = 190) indicated strong statistical evidence for the interactio... | DisGeNET | Detail |
| Results from the recruited cohort (n = 190) indicated strong statistical evidence for the interactio... | DisGeNET | Detail |
| Statistically significant risks were observed for HPV16-containing SCC of the cervix with the varian... | DisGeNET | Detail |
| Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs361525, and rs1800610) in... | DisGeNET | Detail |
| Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs361525, and rs1800610) in... | DisGeNET | Detail |
| In this clinical study, the influence of genetic variants of TNF-beta (c.7G>A, IVS1+90G>A, C13... | DisGeNET | Detail |
| Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs361525, and rs1800610) in... | 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
- chr6:31,572,779-31,572,779
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1164
- Mean of sample read depth (HGVD)
- 230.71
- Standard deviation of sample read depth (HGVD)
- 103.04
- Number of reference allele (HGVD)
- 1969
- Number of alternative allele (HGVD)
- 359
- Allele Frequency (HGVD)
- 0.15420962199312716
- Gene Symbol (HGVD)
- LTA
- 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))
- rs2229094
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1867
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 3129
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16758
- East Asian Chromosome Counts (ExAC)
- 8476
- East Asian Allele Counts (ExAC)
- 1678
- East Asian Heterozygous Counts (ExAC)
- 1378
- East Asian Homozygous Counts (ExAC)
- 150
- East Asian Allele Frequency (ExAC)
- 0.1979707409155262
- Chromosome Counts in All Race (ExAC)
- 116038
- Allele Counts in All Race (ExAC)
- 31537
- Heterozygous Counts in All Race (ExAC)
- 22749
- Homozygous Counts in All Race (ExAC)
- 4394
- Allele Frequency in All Race (ExAC)
- 0.27178165773281165
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