chr19:11131368:G>A Detail (hg38) (LDLR)

Information

Genome

Assembly Position
hg19 chr19:11,242,044-11,242,044 View the variant detail on this assembly version.
hg38 chr19:11,131,368-11,131,368

HGVS

Type Transcript Protein
RefSeq NM_001195800.1:c.*52G>A
NM_001195799.1:c.*52G>A
NM_001195803.1:c.*52G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.411
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.394

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 tgv61201153 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 2018-06-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Coinfection The aim of this study was to assess the impact of the genetic pattern (GP) defin... BeFree 23715768 Detail
0.002 Coinfection The aim of this study was to assess the impact of the genetic pattern (GP) defin... BeFree 23715768 Detail
0.020 HIV Infections Variations in rs14158 are associated with SVR to Peg-IFN and RBV in HIV/HCV-coin... BeFree 21572301 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000527.5(LDLR):c.*52G>A AND Hypercholesterolemia, familial, 1 ClinVar Detail
NM_000527.5(LDLR):c.*52G>A AND not provided ClinVar Detail
The aim of this study was to assess the impact of the genetic pattern (GP) defined by the single nuc... DisGeNET Detail
The aim of this study was to assess the impact of the genetic pattern (GP) defined by the single nuc... DisGeNET Detail
Variations in rs14158 are associated with SVR to Peg-IFN and RBV in HIV/HCV-coinfected patients harb... 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
rs14158 dbSNP
Genome
hg38
Position
chr19:11,131,368-11,131,368
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs14158
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4113
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6894
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8606
East Asian Allele Counts (ExAC)
3392
East Asian Heterozygous Counts (ExAC)
2134
East Asian Homozygous Counts (ExAC)
629
East Asian Allele Frequency (ExAC)
0.3941436207297235
Chromosome Counts in All Race (ExAC)
121100
Allele Counts in All Race (ExAC)
29838
Heterozygous Counts in All Race (ExAC)
22046
Homozygous Counts in All Race (ExAC)
3896
Allele Frequency in All Race (ExAC)
0.24639141205615195
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