chr19:11100236:C>T Detail (hg38) (LDLR)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr19:11,210,912-11,210,912 View the variant detail on this assembly version. |
hg38 | chr19:11,100,236-11,100,236 |
HGVS
Type | Transcript | Protein |
---|---|---|
RefSeq | NM_001195800.1:c.81C>T | NP_001182729.1:p.Cys27= |
NM_001195799.1:c.81C>T | NP_001182728.1:p.Cys27= | |
NM_001195803.1:c.81C>T | NP_001182732.1:p.Cys27= |
Summary
MGeND
Clinical significance | |
Variant entry | |
GWAS entry | |
Disease area statistics | Show details |
Frequency
JP | HGVD:0.004 |
ToMMo:0.001 | |
NCBN:[No Data.] | |
NCBN(Hondo):[No Data.] | |
NCBN(Ryukyu):[No Data.] | |
East asia | ExAC:0.009 |
Prediction
ClinVar
Clinical Significance |
![]() |
Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
---|---|---|---|---|---|
![]() |
2021-06-10 | criteria provided, multiple submitters, no conflicts | Hypercholesterolemia, familial, 1 |
![]() |
Detail |
![]() |
2016-11-02 | criteria provided, multiple submitters, no conflicts | not specified |
![]() |
Detail |
![]() |
2020-09-16 | no assertion criteria provided | Smith-Lemli-Opitz syndrome |
![]() |
Detail |
![]() |
2024-02-01 | criteria provided, single submitter | familial hypercholesterolemia |
![]() |
Detail |
![]() |
2015-12-08 | criteria provided, single submitter |
![]() |
Detail |
CIViC
[No Data.]
DisGeNET
Score | Disease name | Description | Source | Pubmed | Links |
---|---|---|---|---|---|
0.167 | Coronary heart disease | Meta-analysis of low density lipoprotein receptor (LDLR) rs2228671 polymorphism ... | BeFree | 24900971 | Detail |
0.019 | Coronary Arteriosclerosis | Meta-analysis of low density lipoprotein receptor (LDLR) rs2228671 polymorphism ... | BeFree | 24900971 | 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.81C>T (p.Cys27=) AND Hypercholesterolemia, familial, 1 | ClinVar | Detail |
NM_000527.5(LDLR):c.81C>T (p.Cys27=) AND not specified | ClinVar | Detail |
NM_000527.5(LDLR):c.81C>T (p.Cys27=) AND Smith-Lemli-Opitz syndrome | ClinVar | Detail |
NM_000527.5(LDLR):c.81C>T (p.Cys27=) AND Familial hypercholesterolemia | ClinVar | Detail |
NM_000527.5(LDLR):c.81C>T (p.Cys27=) AND Cardiovascular phenotype | ClinVar | Detail |
Meta-analysis of low density lipoprotein receptor (LDLR) rs2228671 polymorphism and coronary heart d... | DisGeNET | Detail |
Meta-analysis of low density lipoprotein receptor (LDLR) rs2228671 polymorphism and coronary heart d... | 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
- rs2228671 dbSNP
- Genome
- hg38
- Position
- chr19:11,100,236-11,100,236
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 94.67
- Standard deviation of sample read depth (HGVD)
- 48.79
- Number of reference allele (HGVD)
- 2410
- Number of alternative allele (HGVD)
- 10
- Allele Frequency (HGVD)
- 0.004132231404958678
- 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))
- rs2228671
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.001
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8634
- East Asian Allele Counts (ExAC)
- 75
- East Asian Heterozygous Counts (ExAC)
- 75
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.008686587908269632
- Chromosome Counts in All Race (ExAC)
- 121058
- Allele Counts in All Race (ExAC)
- 10484
- Heterozygous Counts in All Race (ExAC)
- 9398
- Homozygous Counts in All Race (ExAC)
- 543
- Allele Frequency in All Race (ExAC)
- 0.0866031158618183
Genome browser