chr1:3424388:G>A Detail (hg19) (MEGF6)

Information

Genome

Assembly Position
hg19 chr1:3,424,388-3,424,388
hg38 chr1:3,507,824-3,507,824 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001409.3:c.1760C>T NP_001400.3:p.Pro587Leu
Ensemble ENST00000356575.9:c.1760C>T ENST00000356575.9:p.Pro587Leu
ENST00000294599.8:c.1445C>T ENST00000294599.8:p.Pro482Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.062
ToMMo:0.062
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.051

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 604266 OMIM
HGNC 3232 HGNC
Ensembl ENSG00000162591 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv127825 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
0.003 liver carcinoma Seven polymorphisms of caspase 9 (rs2308941)C-->T and DOK2(rs2242241) T-->... BeFree 16109524 Detail
<0.001 liver carcinoma Seven polymorphisms of caspase 9 (rs2308941)C--&gt;T and DOK2(rs2242241) T--&gt;... BeFree 16109524 Detail
Annotation

Annotations

DescrptionSourceLinks
Seven polymorphisms of caspase 9 (rs2308941)C--&gt;T and DOK2(rs2242241) T--&gt;G, 6 of polymorphism... DisGeNET Detail
Seven polymorphisms of caspase 9 (rs2308941)C--&gt;T and DOK2(rs2242241) T--&gt;G, 6 of polymorphism... 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
hg19
Position
chr1:3,424,388-3,424,388
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
836
Mean of sample read depth (HGVD)
13.95
Standard deviation of sample read depth (HGVD)
18.20
Number of reference allele (HGVD)
1568
Number of alternative allele (HGVD)
103
Allele Frequency (HGVD)
0.061639736684619986
Gene Symbol (HGVD)
MEGF6
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))
rs947345
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0625
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1047
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8584
East Asian Allele Counts (ExAC)
435
East Asian Heterozygous Counts (ExAC)
421
East Asian Homozygous Counts (ExAC)
7
East Asian Allele Frequency (ExAC)
0.05067567567567568
Chromosome Counts in All Race (ExAC)
119168
Allele Counts in All Race (ExAC)
5682
Heterozygous Counts in All Race (ExAC)
5346
Homozygous Counts in All Race (ExAC)
168
Allele Frequency in All Race (ExAC)
0.047680585392051555
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