chr6:160540105:T>C Detail (hg38) (LPA)

Information

Genome

Assembly Position
hg19 chr6:160,961,137-160,961,137 View the variant detail on this assembly version.
hg38 chr6:160,540,105-160,540,105

HGVS

Type Transcript Protein
RefSeq NM_005577.2:c.5673A>G NP_005568.2:p.Ile1891Met
Ensemble ENST00000316300.10:c.5673A>G ENST00000316300.10:p.Ile1891Met
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.093
ToMMo:0.101
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.090

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 152200 OMIM
HGNC 6667 HGNC
Ensembl ENSG00000198670 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv27710355 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2020-08-07 no assertion criteria provided LIPOPROTEIN(a) POLYMORPHISM germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.150 coronary artery disease In conclusion, heritable contributions of LPA rs10455872 and rs3798220 to Lp(a) ... BeFree 23735648 Detail
0.150 coronary artery disease Genetic variants in the rs3798220, rs10455872 and rs6415084 single-nucleotide po... BeFree 23978127 Detail
0.010 Coronary heart disease Single nucleotide polymorphisms (SNPs) at the KIF6 (kinesin like protein 6, rs20... BeFree 22192511 Detail
0.001 Coronary heart disease Single nucleotide polymorphisms (SNPs) at the KIF6 (kinesin like protein 6, rs20... BeFree 22192511 Detail
0.272 Coronary heart disease Large-scale association analysis identifies 13 new susceptibility loci for coron... GWASCAT 21378990 Detail
0.150 coronary artery disease [Large-scale association analysis identifies 13 new susceptibility loci for coro... GAD 21378990 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005577.4(LPA):c.5673A>G (p.Ile1891Met) AND LIPOPROTEIN(a) POLYMORPHISM ClinVar Detail
In conclusion, heritable contributions of LPA rs10455872 and rs3798220 to Lp(a) cholesterol levels a... DisGeNET Detail
Genetic variants in the rs3798220, rs10455872 and rs6415084 single-nucleotide polymorphisms (SNPs) i... DisGeNET Detail
Single nucleotide polymorphisms (SNPs) at the KIF6 (kinesin like protein 6, rs20455 or 719Arg), LPA ... DisGeNET Detail
Single nucleotide polymorphisms (SNPs) at the KIF6 (kinesin like protein 6, rs20455 or 719Arg), LPA ... DisGeNET Detail
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. DisGeNET Detail
[Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.... 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
rs3798220 dbSNP
Genome
hg38
Position
chr6:160,540,105-160,540,105
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
137.96
Standard deviation of sample read depth (HGVD)
61.38
Number of reference allele (HGVD)
2195
Number of alternative allele (HGVD)
224
Allele Frequency (HGVD)
0.09260024803637867
Gene Symbol (HGVD)
LPA
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))
rs3798220
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1012
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1696
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8638
East Asian Allele Counts (ExAC)
776
East Asian Heterozygous Counts (ExAC)
696
East Asian Homozygous Counts (ExAC)
40
East Asian Allele Frequency (ExAC)
0.08983561009492938
Chromosome Counts in All Race (ExAC)
121388
Allele Counts in All Race (ExAC)
5444
Heterozygous Counts in All Race (ExAC)
4242
Homozygous Counts in All Race (ExAC)
601
Allele Frequency in All Race (ExAC)
0.04484792565986753
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