chr4:109717654:C>T Detail (hg38) (PLA2G12A)

Information

Genome

Assembly Position
hg19 chr4:110,638,810-110,638,810 View the variant detail on this assembly version.
hg38 chr4:109,717,654-109,717,654

HGVS

Type Transcript Protein
RefSeq NM_030821.4:c.345G>A NP_110448.2:p.Glu115=
Ensemble ENST00000243501.10:c.345G>A ENST00000243501.10:p.Glu115=
ENST00000502283.1:c.339G>A ENST00000502283.1:p.Glu113=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.212
ToMMo:0.227
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.228

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 611652 OMIM
HGNC 18554 HGNC
Ensembl ENSG00000123739 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv18227366 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.129 age related macular degeneration [Genetic variants near TIMP3 and high-density lipoprotein-associated loci influe... GAD 20385819 Detail
0.006 Exudative age-related macular degeneration Suggestive association between PLA2G12A single nucleotide polymorphism rs2285714... BeFree 23112570 Detail
0.129 age related macular degeneration Genetic variants near TIMP3 and high-density lipoprotein-associated loci influen... GWASCAT 20385819 Detail
0.129 age related macular degeneration NA GAD Detail
Annotation

Annotations

DescrptionSourceLinks
[Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility t... DisGeNET Detail
Suggestive association between PLA2G12A single nucleotide polymorphism rs2285714 and response to ant... DisGeNET Detail
Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to... DisGeNET Detail
NA 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
-
Genome
hg38
Position
chr4:109,717,654-109,717,654
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1136
Mean of sample read depth (HGVD)
44.26
Standard deviation of sample read depth (HGVD)
27.71
Number of reference allele (HGVD)
1789
Number of alternative allele (HGVD)
482
Allele Frequency (HGVD)
0.21224130339057684
Gene Symbol (HGVD)
PLA2G12A
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))
rs2285714
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2269
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3803
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
1974
East Asian Heterozygous Counts (ExAC)
1504
East Asian Homozygous Counts (ExAC)
235
East Asian Allele Frequency (ExAC)
0.22841934737329322
Chromosome Counts in All Race (ExAC)
121386
Allele Counts in All Race (ExAC)
45212
Heterozygous Counts in All Race (ExAC)
26814
Homozygous Counts in All Race (ExAC)
9199
Allele Frequency in All Race (ExAC)
0.3724646993887269
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