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 Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606945 OMIM
HGNC 6547 HGNC
Ensembl ENSG00000130164 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv61197745 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-06-10 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, familial, 1 germline Detail
Benign 2016-11-02 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2020-09-16 no assertion criteria provided Smith-Lemli-Opitz syndrome germline Detail
Benign 2024-02-01 criteria provided, single submitter familial hypercholesterolemia germline Detail
Benign 2015-12-08 criteria provided, single submitter germline 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

DescrptionSourceLinks
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