chr6:31962685:G>A Detail (hg38) (SKIC2, LOC126859653)

Information

Genome

Assembly Position
hg19 chr6:31,930,462-31,930,462 View the variant detail on this assembly version.
hg38 chr6:31,962,685-31,962,685

HGVS

Type Transcript Protein
RefSeq NM_006929.4:c.1212-29G>A
Ensemble ENST00000375394.7:c.1212-29G>A
ENST00000491994.2:c.1212-29G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.126
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.078

Prediction

ClinVar

Clinical Significance not provided
Review star
Show details
Links
Type Database ID Link
Gene MIM 600478 OMIM
HGNC 10898 HGNC
Ensembl ENSG00000204351 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24806102 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
not provided no assertion provided not provided not provided Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.007 macular degeneration After adjusting for age, gender, ARMS2 A69S, and CFHI62V, the A allele of rs4296... BeFree 24865191 Detail
0.404 age related macular degeneration After adjusting for age, gender, ARMS2 A69S, and CFHI62V, the A allele of rs4296... BeFree 24865191 Detail
0.131 age related macular degeneration NA GAD Detail
0.131 age related macular degeneration [Genome-wide association identifies SKIV2L and MYRIP as protective factors for a... GAD 20861866 Detail
0.125 age related macular degeneration The SKIV2L SNPs rs429608 and rs453821 were significantly associated with neovasc... BeFree 23260260 Detail
0.131 age related macular degeneration Genome-wide association identifies SKIV2L and MYRIP as protective factors for ag... GWASCAT 20861866 Detail
0.131 age related macular degeneration Seven new loci associated with age-related macular degeneration. GWASCAT 23455636 Detail
0.131 age related macular degeneration Genetic variants near TIMP3 and high-density lipoprotein-associated loci influen... GWASCAT 20385819 Detail
0.131 age related macular degeneration [Genetic variants near TIMP3 and high-density lipoprotein-associated loci influe... GAD 20385819 Detail
<0.001 macular degeneration The SKIV2L SNPs rs429608 and rs453821 were significantly associated with neovasc... BeFree 23260260 Detail
0.131 age related macular degeneration Genotype distribution of rs1061170 (CFH), rs429608 (SKIV2L), rs2679798 (MYRIP) a... BeFree 24995509 Detail
0.267 age related macular degeneration The association of SKIV2L rs429608 with neovascular AMD remained significant aft... BeFree 23260260 Detail
0.480 age related macular degeneration The association of SKIV2L rs429608 with neovascular AMD remained significant aft... BeFree 23260260 Detail
0.005 macular degeneration The association of SKIV2L rs429608 with neovascular AMD remained significant aft... BeFree 23260260 Detail
0.011 macular degeneration The association of SKIV2L rs429608 with neovascular AMD remained significant aft... BeFree 23260260 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_006929.5(SKIC2):c.1212-29G>A AND not provided ClinVar Detail
After adjusting for age, gender, ARMS2 A69S, and CFHI62V, the A allele of rs429608 was significantly... DisGeNET Detail
After adjusting for age, gender, ARMS2 A69S, and CFHI62V, the A allele of rs429608 was significantly... DisGeNET Detail
NA DisGeNET Detail
[Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular d... DisGeNET Detail
The SKIV2L SNPs rs429608 and rs453821 were significantly associated with neovascular AMD (P = 7.39 ×... DisGeNET Detail
Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular de... DisGeNET Detail
Seven new loci associated with age-related macular degeneration. DisGeNET Detail
Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to... DisGeNET Detail
[Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility t... DisGeNET Detail
The SKIV2L SNPs rs429608 and rs453821 were significantly associated with neovascular AMD (P = 7.39 ×... DisGeNET Detail
Genotype distribution of rs1061170 (CFH), rs429608 (SKIV2L), rs2679798 (MYRIP) and both rs11549465 a... DisGeNET Detail
The association of SKIV2L rs429608 with neovascular AMD remained significant after adjusting for CFH... DisGeNET Detail
The association of SKIV2L rs429608 with neovascular AMD remained significant after adjusting for CFH... DisGeNET Detail
The association of SKIV2L rs429608 with neovascular AMD remained significant after adjusting for CFH... DisGeNET Detail
The association of SKIV2L rs429608 with neovascular AMD remained significant after adjusting for CFH... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs429608 dbSNP
Genome
hg38
Position
chr6:31,962,685-31,962,685
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))
rs429608
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1263
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2117
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8572
East Asian Allele Counts (ExAC)
670
East Asian Heterozygous Counts (ExAC)
596
East Asian Homozygous Counts (ExAC)
37
East Asian Allele Frequency (ExAC)
0.07816145590293981
Chromosome Counts in All Race (ExAC)
117666
Allele Counts in All Race (ExAC)
17232
Heterozygous Counts in All Race (ExAC)
14398
Homozygous Counts in All Race (ExAC)
1417
Allele Frequency in All Race (ExAC)
0.14644842180408954
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