chr20:36932660:C>T Detail (hg19) (BPI)

Information

Genome

Assembly Position
hg19 chr20:36,932,660-36,932,660
hg38 chr20:38,304,258-38,304,258 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001725.2:c.47C>T NP_001716.2:p.Ala16Val
Ensemble ENST00000262865.9:c.47C>T ENST00000262865.9:p.Ala16Val
ENST00000642449.2:c.35C>T ENST00000642449.2:p.Ala12Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.650
ToMMo:0.658
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.554

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 109195 OMIM
HGNC 1095 HGNC
Ensembl ENSG00000101425 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv63677051 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-28 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Septicaemia due to gram-negative organism, unspecified Genotype AG of rs1800629 (the LTA gene) and genotypes CC and CT of rs1341023 (th... BeFree 25000179 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001725.3(BPI):c.35C>T (p.Ala12Val) AND not specified ClinVar Detail
Genotype AG of rs1800629 (the LTA gene) and genotypes CC and CT of rs1341023 (the BPI gene) were ass... 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
rs1341023 dbSNP
Genome
hg19
Position
chr20:36,932,660-36,932,660
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
186.89
Standard deviation of sample read depth (HGVD)
85.97
Number of reference allele (HGVD)
847
Number of alternative allele (HGVD)
1573
Allele Frequency (HGVD)
0.65
Gene Symbol (HGVD)
BPI
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))
rs1341023
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6578
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11024
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8594
East Asian Allele Counts (ExAC)
4757
East Asian Heterozygous Counts (ExAC)
2101
East Asian Homozygous Counts (ExAC)
1328
East Asian Allele Frequency (ExAC)
0.5535257156155458
Chromosome Counts in All Race (ExAC)
120538
Allele Counts in All Race (ExAC)
61014
Heterozygous Counts in All Race (ExAC)
28898
Homozygous Counts in All Race (ExAC)
16058
Allele Frequency in All Race (ExAC)
0.5061806235378055
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