chr6:160961137:T>C Detail (hg19) (LPA)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:160,961,137-160,961,137 |
| hg38 | chr6:160,540,105-160,540,105 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_005577.2:c.5673A>G | NP_005568.2:p.Ile1891Met |
| Ensemble | ENST00000316300.10:c.5673A>G | ENST00000316300.10:p.Ile1891Met |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.093 |
| ToMMo:0.101 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.090 |
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 |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2020-08-07 | no assertion criteria provided | LIPOPROTEIN(a) POLYMORPHISM |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.150 | coronary artery disease | In conclusion, heritable contributions of LPA rs10455872 and rs3798220 to Lp(a) ... | BeFree | 23735648 | Detail |
| 0.150 | coronary artery disease | Genetic variants in the rs3798220, rs10455872 and rs6415084 single-nucleotide po... | BeFree | 23978127 | Detail |
| 0.010 | Coronary heart disease | Single nucleotide polymorphisms (SNPs) at the KIF6 (kinesin like protein 6, rs20... | BeFree | 22192511 | Detail |
| 0.001 | Coronary heart disease | Single nucleotide polymorphisms (SNPs) at the KIF6 (kinesin like protein 6, rs20... | BeFree | 22192511 | Detail |
| 0.272 | Coronary heart disease | Large-scale association analysis identifies 13 new susceptibility loci for coron... | GWASCAT | 21378990 | Detail |
| 0.150 | coronary artery disease | [Large-scale association analysis identifies 13 new susceptibility loci for coro... | GAD | 21378990 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_005577.4(LPA):c.5673A>G (p.Ile1891Met) AND LIPOPROTEIN(a) POLYMORPHISM | ClinVar | Detail |
| In conclusion, heritable contributions of LPA rs10455872 and rs3798220 to Lp(a) cholesterol levels a... | DisGeNET | Detail |
| Genetic variants in the rs3798220, rs10455872 and rs6415084 single-nucleotide polymorphisms (SNPs) i... | DisGeNET | Detail |
| Single nucleotide polymorphisms (SNPs) at the KIF6 (kinesin like protein 6, rs20455 or 719Arg), LPA ... | DisGeNET | Detail |
| Single nucleotide polymorphisms (SNPs) at the KIF6 (kinesin like protein 6, rs20455 or 719Arg), LPA ... | DisGeNET | Detail |
| Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. | DisGeNET | Detail |
| [Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.... | 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
- rs3798220 dbSNP
- Genome
- hg19
- Position
- chr6:160,961,137-160,961,137
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 137.96
- Standard deviation of sample read depth (HGVD)
- 61.38
- Number of reference allele (HGVD)
- 2195
- Number of alternative allele (HGVD)
- 224
- Allele Frequency (HGVD)
- 0.09260024803637867
- Gene Symbol (HGVD)
- LPA
- 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))
- rs3798220
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1012
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1696
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8638
- East Asian Allele Counts (ExAC)
- 776
- East Asian Heterozygous Counts (ExAC)
- 696
- East Asian Homozygous Counts (ExAC)
- 40
- East Asian Allele Frequency (ExAC)
- 0.08983561009492938
- Chromosome Counts in All Race (ExAC)
- 121388
- Allele Counts in All Race (ExAC)
- 5444
- Heterozygous Counts in All Race (ExAC)
- 4242
- Homozygous Counts in All Race (ExAC)
- 601
- Allele Frequency in All Race (ExAC)
- 0.04484792565986753
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