chr19:11116926:C>T Detail (hg38) (LDLR)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr19:11,227,602-11,227,602 View the variant detail on this assembly version. |
| hg38 | chr19:11,116,926-11,116,926 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001195800.1:c.1269C>T | NP_001182729.1:p.Asn423= |
| NM_001195799.1:c.1650C>T | NP_001182728.1:p.Asn550= | |
| NM_001195803.1:c.1392C>T | NP_001182732.1:p.Asn464= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.129 |
| ToMMo:0.123 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.176 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2015-12-31 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
Likely benign
|
2023-03-30 | criteria provided, multiple submitters, no conflicts | Hypercholesterolemia, familial, 1 |
germline
unknown
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | familial hypercholesterolemia |
germline
|
Detail |
|
Benign
|
2023-11-29 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2015-12-08 | criteria provided, single submitter |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.003 | cerebral infarction | The LDLR analysis based on the haplotypes rs688 and rs5925 was conducted in a Ta... | BeFree | 22621231 | Detail |
| 0.018 | Cerebrovascular accident | The LDLR analysis based on the haplotypes rs688 and rs5925 was conducted in a Ta... | BeFree | 22621231 | Detail |
| 0.291 | Hypertensive disease | Our results not only demonstrated potential interactions of APOE epsilon2/epsilo... | BeFree | 18851860 | Detail |
| 0.152 | Cardiovascular Diseases | In a previous study, analysis of the genetic LDLR variant rs688 provided evidenc... | BeFree | 24295502 | Detail |
| 0.035 | Alzheimer's disease | We previously identified a single nucleotide polymorphism (SNP), rs688:C>T, t... | BeFree | 20232416 | Detail |
| 0.123 | Coronary heart disease | The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARC... | BeFree | 20810930 | Detail |
| <0.001 | Coronary Arteriosclerosis | The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARC... | BeFree | 20810930 | Detail |
| 0.126 | coronary artery disease | The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARC... | BeFree | 20810930 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND not specified | ClinVar | Detail |
| NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND Hypercholesterolemia, familial, 1 | ClinVar | Detail |
| NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND Familial hypercholesterolemia | ClinVar | Detail |
| NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND not provided | ClinVar | Detail |
| NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND Cardiovascular phenotype | ClinVar | Detail |
| The LDLR analysis based on the haplotypes rs688 and rs5925 was conducted in a Taiwanese population a... | DisGeNET | Detail |
| The LDLR analysis based on the haplotypes rs688 and rs5925 was conducted in a Taiwanese population a... | DisGeNET | Detail |
| Our results not only demonstrated potential interactions of APOE epsilon2/epsilon3/epsilon4 and LDLR... | DisGeNET | Detail |
| In a previous study, analysis of the genetic LDLR variant rs688 provided evidence suggesting that ge... | DisGeNET | Detail |
| We previously identified a single nucleotide polymorphism (SNP), rs688:C>T, that modulates LDLR e... | DisGeNET | Detail |
| The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARCA4-LDLR gene locus (... | DisGeNET | Detail |
| The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARCA4-LDLR gene locus (... | DisGeNET | Detail |
| The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARCA4-LDLR gene locus (... | 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
- rs688 dbSNP
- Genome
- hg38
- Position
- chr19:11,116,926-11,116,926
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 109.90
- Standard deviation of sample read depth (HGVD)
- 53.94
- Number of reference allele (HGVD)
- 2107
- Number of alternative allele (HGVD)
- 313
- Allele Frequency (HGVD)
- 0.12933884297520662
- Gene Symbol (HGVD)
- LDLR
- 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))
- rs688
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1233
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 2066
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8648
- East Asian Allele Counts (ExAC)
- 1525
- East Asian Heterozygous Counts (ExAC)
- 1267
- East Asian Homozygous Counts (ExAC)
- 129
- East Asian Allele Frequency (ExAC)
- 0.1763413506012951
- Chromosome Counts in All Race (ExAC)
- 121396
- Allele Counts in All Race (ExAC)
- 45902
- Heterozygous Counts in All Race (ExAC)
- 26978
- Homozygous Counts in All Race (ExAC)
- 9462
- Allele Frequency in All Race (ExAC)
- 0.37811789515305283
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