chr19:11230881:T>C Detail (hg19) (LDLR)

Information

Genome

Assembly Position
hg19 chr19:11,230,881-11,230,881
hg38 chr19:11,120,205-11,120,205 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001195800.1:c.1455T>C NP_001182729.1:p.Val485=
NM_001195799.1:c.1836T>C NP_001182728.1:p.Val612=
NM_001195803.1:c.1578T>C NP_001182732.1:p.Val526=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.177
ToMMo:0.175
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.220

Prediction

ClinVar

Clinical Significance Benign Likely 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 tgv61200279 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2021-06-10 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, familial, 1 germline Detail
Benign 2018-02-07 criteria provided, multiple submitters, no conflicts not specified germline 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
<0.001 Hashimoto Disease We analyzed the associations of seven polymorphisms of genes involved in lipid m... BeFree 25587205 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000527.5(LDLR):c.1959T>C (p.Val653=) AND Hypercholesterolemia, familial, 1 ClinVar Detail
NM_000527.5(LDLR):c.1959T>C (p.Val653=) AND not specified ClinVar Detail
NM_000527.5(LDLR):c.1959T>C (p.Val653=) AND Familial hypercholesterolemia ClinVar Detail
NM_000527.5(LDLR):c.1959T>C (p.Val653=) AND not provided ClinVar Detail
NM_000527.5(LDLR):c.1959T>C (p.Val653=) 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
We analyzed the associations of seven polymorphisms of genes involved in lipid metabolism (APOA5 rs3... 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
rs5925 dbSNP
Genome
hg19
Position
chr19:11,230,881-11,230,881
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
194.75
Standard deviation of sample read depth (HGVD)
87.01
Number of reference allele (HGVD)
1992
Number of alternative allele (HGVD)
428
Allele Frequency (HGVD)
0.1768595041322314
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))
rs5925
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1752
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2936
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8626
East Asian Allele Counts (ExAC)
1902
East Asian Heterozygous Counts (ExAC)
1494
East Asian Homozygous Counts (ExAC)
204
East Asian Allele Frequency (ExAC)
0.22049617435659633
Chromosome Counts in All Race (ExAC)
121264
Allele Counts in All Race (ExAC)
49618
Heterozygous Counts in All Race (ExAC)
28210
Homozygous Counts in All Race (ExAC)
10704
Allele Frequency in All Race (ExAC)
0.4091733737960153
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