chr6:31930441:G>T Detail (hg19) (SKIC2, LOC126859653)

Information

Genome

Assembly Position
hg19 chr6:31,930,441-31,930,441
hg38 chr6:31,962,664-31,962,664 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_006929.4:c.1212-50G>T
Ensemble ENST00000375394.7:c.1212-50G>T
ENST00000491994.2:c.1212-50G>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.415
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.570

Prediction

ClinVar

Clinical Significance Benign
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 tgv24806094 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.131 age related macular degeneration NA GAD Detail
0.120 Infant length A novel common variant in DCST2 is associated with length in early life and heig... GWASCAT 25281659 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_006929.5(SKIC2):c.1212-50G>T AND not provided ClinVar Detail
NA DisGeNET Detail
A novel common variant in DCST2 is associated with length in early life and height in adulthood. DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs592229 dbSNP
Genome
hg19
Position
chr6:31,930,441-31,930,441
Variant Type
snv
Reference Allele
G
Alternative Allele
T
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))
rs592229
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4153
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6960
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8520
East Asian Allele Counts (ExAC)
4860
East Asian Heterozygous Counts (ExAC)
2088
East Asian Homozygous Counts (ExAC)
1386
East Asian Allele Frequency (ExAC)
0.5704225352112676
Chromosome Counts in All Race (ExAC)
117558
Allele Counts in All Race (ExAC)
72155
Heterozygous Counts in All Race (ExAC)
27049
Homozygous Counts in All Race (ExAC)
22551
Allele Frequency in All Race (ExAC)
0.6137821330747376
Genome browser