chr17:45360730:T>C Detail (hg19) (ITGB3)

Information

Genome

Assembly Position
hg19 chr17:45,360,730-45,360,730
hg38 chr17:47,283,364-47,283,364 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000212.2:c.176T>C NP_000203.2:p.Leu59Pro
Ensemble ENST00000559488.7:c.176T>C ENST00000559488.7:p.Leu59Pro
ENST00000571680.1:c.176T>C ENST00000571680.1:p.Leu59Pro
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.004
ToMMo:0.003
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.003

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 173470 OMIM
HGNC 6156 HGNC
Ensembl ENSG00000259207 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57962094 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2007-01-01 no assertion criteria provided PL(A1)/(A2) ALLOANTIGEN POLYMORPHISM germline Detail
Benign 2017-05-31 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2020-06-18 reviewed by expert panel Glanzmann thrombasthenia germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
risk factor 2007-01-01 no assertion criteria provided Myocardial infarction, susceptibility to germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Ischemic stroke Impact of COX-2 rs5275 and rs20417 and GPIIIa rs5918 polymorphisms on 90-day isc... BeFree 20472470 Detail
0.130 Cerebrovascular accident This is the first study to demonstrate associations between stroke functional ou... BeFree 20472470 Detail
0.002 Ischemic Cerebrovascular Accident Impact of COX-2 rs5275 and rs20417 and GPIIIa rs5918 polymorphisms on 90-day isc... BeFree 20472470 Detail
0.120 Posttransfusion purpura NA CLINVAR Detail
0.393 myocardial infarction NA CLINVAR Detail
0.120 FRACTURE, HIP, SUSCEPTIBILITY TO (finding) NA CLINVAR Detail
0.003 Malignant neoplasm of ovary A functional Leu33Pro polymorphism (rs5918) in the beta(3) subunit of the integr... BeFree 19876733 Detail
0.003 ovarian carcinoma A functional Leu33Pro polymorphism (rs5918) in the beta(3) subunit of the integr... BeFree 19876733 Detail
<0.001 Exercise-induced angina An SNP in ITGB3 (Leu59Pro, rs5918) was slightly, but not significantly (P = .083... BeFree 18035074 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND PL(A1)/(A2) ALLOANTIGEN POLYMORPHISM ClinVar Detail
NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND not specified ClinVar Detail
NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND Glanzmann thrombasthenia ClinVar Detail
NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND not provided ClinVar Detail
NM_000212.3(ITGB3):c.176T>C (p.Leu59Pro) AND Myocardial infarction, susceptibility to ClinVar Detail
Impact of COX-2 rs5275 and rs20417 and GPIIIa rs5918 polymorphisms on 90-day ischemic stroke functio... DisGeNET Detail
This is the first study to demonstrate associations between stroke functional outcome and 2 COX-2 va... DisGeNET Detail
Impact of COX-2 rs5275 and rs20417 and GPIIIa rs5918 polymorphisms on 90-day ischemic stroke functio... DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
A functional Leu33Pro polymorphism (rs5918) in the beta(3) subunit of the integrin gene (ITGB3) has ... DisGeNET Detail
A functional Leu33Pro polymorphism (rs5918) in the beta(3) subunit of the integrin gene (ITGB3) has ... DisGeNET Detail
An SNP in ITGB3 (Leu59Pro, rs5918) was slightly, but not significantly (P = .083), more common among... 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
rs5918 dbSNP
Genome
hg19
Position
chr17:45,360,730-45,360,730
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
78.97
Standard deviation of sample read depth (HGVD)
36.12
Number of reference allele (HGVD)
2406
Number of alternative allele (HGVD)
10
Allele Frequency (HGVD)
0.0041390728476821195
Gene Symbol (HGVD)
ITGB3
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))
rs5918
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.003
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
51
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
27
East Asian Heterozygous Counts (ExAC)
25
East Asian Homozygous Counts (ExAC)
1
East Asian Allele Frequency (ExAC)
0.0031242767877806064
Chromosome Counts in All Race (ExAC)
120916
Allele Counts in All Race (ExAC)
14938
Heterozygous Counts in All Race (ExAC)
12838
Homozygous Counts in All Race (ExAC)
1050
Allele Frequency in All Race (ExAC)
0.1235403089748255
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