chr20:38373117:T>C Detail (hg38) (LBP)

Information

Genome

Assembly Position
hg19 chr20:37,001,761-37,001,761 View the variant detail on this assembly version.
hg38 chr20:38,373,117-38,373,117

HGVS

Type Transcript Protein
RefSeq NM_004139.4:c.1306T>C NP_004130.2:p.Phe436Leu
Ensemble ENST00000217407.3:c.1306T>C ENST00000217407.3:p.Phe436Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.039
ToMMo:0.029
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.046

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 151990 OMIM
HGNC 6517 HGNC
Ensembl ENSG00000129988 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv63679913 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 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
<0.001 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
<0.001 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
<0.001 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
<0.001 Organ dysfunction syndrome We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... BeFree 24383711 Detail
Annotation

Annotations

DescrptionSourceLinks
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... DisGeNET Detail
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... DisGeNET Detail
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... DisGeNET Detail
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... DisGeNET Detail
We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... 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
chr20:38,373,117-38,373,117
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1205
Mean of sample read depth (HGVD)
155.88
Standard deviation of sample read depth (HGVD)
69.77
Number of reference allele (HGVD)
2316
Number of alternative allele (HGVD)
94
Allele Frequency (HGVD)
0.03900414937759336
Gene Symbol (HGVD)
LBP
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))
rs2232618
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0286
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
479
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
397
East Asian Heterozygous Counts (ExAC)
383
East Asian Homozygous Counts (ExAC)
7
East Asian Allele Frequency (ExAC)
0.04590656799259944
Chromosome Counts in All Race (ExAC)
121360
Allele Counts in All Race (ExAC)
11707
Heterozygous Counts in All Race (ExAC)
10207
Homozygous Counts in All Race (ExAC)
750
Allele Frequency in All Race (ExAC)
0.0964650626235992
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