chr8:6877901:C>G Detail (hg38) (DEFB1)

Information

Genome

Assembly Position
hg19 chr8:6,735,423-6,735,423 View the variant detail on this assembly version.
hg38 chr8:6,877,901-6,877,901

HGVS

Type Transcript Protein
RefSeq NM_005218.3:c.-44G>C
Ensemble ENST00000297439.4:c.-44G>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.869
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.881

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 602056 OMIM
HGNC 2766 HGNC
Ensembl ENSG00000164825 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv31984554 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
<0.001 candidiasis Single-nucleotide polymorphisms in three innate immune genes were associated wit... BeFree 24557424 Detail
<0.001 Tuberculosis, extrapulmonary SNP rs1800972 was associated with extrapulmonary tuberculosis (EPTB) in a codomi... BeFree 23953711 Detail
<0.001 leprosy A study was done on the association of three single nucleotide polymorphisms (SN... BeFree 19460328 Detail
Annotation

Annotations

DescrptionSourceLinks
Single-nucleotide polymorphisms in three innate immune genes were associated with development of a C... DisGeNET Detail
SNP rs1800972 was associated with extrapulmonary tuberculosis (EPTB) in a codominant model (genotype... DisGeNET Detail
A study was done on the association of three single nucleotide polymorphisms (SNPs) in the beta-defe... 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
rs1800972 dbSNP
Genome
hg38
Position
chr8:6,877,901-6,877,901
Variant Type
snv
Reference Allele
C
Alternative Allele
G
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))
rs1800972
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8689
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
14563
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8570
East Asian Allele Counts (ExAC)
7551
East Asian Heterozygous Counts (ExAC)
893
East Asian Homozygous Counts (ExAC)
3329
East Asian Allele Frequency (ExAC)
0.8810968494749125
Chromosome Counts in All Race (ExAC)
120542
Allele Counts in All Race (ExAC)
96249
Heterozygous Counts in All Race (ExAC)
18699
Homozygous Counts in All Race (ExAC)
38775
Allele Frequency in All Race (ExAC)
0.7984685835642349
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