chr19:11238548:A>G Detail (hg19) (LDLR)

Information

Genome

Assembly Position
hg19 chr19:11,238,548-11,238,548
hg38 chr19:11,127,872-11,127,872 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001195800.1:c.1808-136A>G
NM_001195799.1:c.2189-136A>G
NM_001195803.1:c.1778-136A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.910
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

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 tgv61200827 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
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.086 coronary artery disease Two SNPs in the Apolipoprotein B (Apo B) gene [rs1042031 and rs1800479], one in ... BeFree 25134189 Detail
0.059 coronary artery disease Two SNPs in the Apolipoprotein B (Apo B) gene [rs1042031 and rs1800479], one in ... BeFree 25134189 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000527.5(LDLR):c.2312-136A>G AND Hypercholesterolemia, familial, 1 ClinVar Detail
Two SNPs in the Apolipoprotein B (Apo B) gene [rs1042031 and rs1800479], one in the Cholesterol Este... DisGeNET Detail
Two SNPs in the Apolipoprotein B (Apo B) gene [rs1042031 and rs1800479], one in the Cholesterol Este... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2569538 dbSNP
Genome
hg19
Position
chr19:11,238,548-11,238,548
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs2569538
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9098
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
15246
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
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