chr19:10274864:A>T Detail (hg38) (ICAM1, LIMASI)

Information

Genome

Assembly Position
hg19 chr19:10,385,540-10,385,540 View the variant detail on this assembly version.
hg38 chr19:10,274,864-10,274,864

HGVS

Type Transcript Protein
RefSeq NM_000201.2:c.167A>T NP_000192.2:p.Lys56Met
Ensemble ENST00000264832.8:c.167A>T ENST00000264832.8:p.Lys56Met
ENST00000423829.2:c.67+3638A>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.069
ToMMo:0.071
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.056

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 147840 OMIM
HGNC 5344 HGNC
Ensembl ENSG00000090339 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv61159666 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2013-09-01 no assertion criteria provided Malaria, cerebral, susceptibility to germline Detail
Benign 2019-12-05 criteria provided, single submitter ICAM1-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.136 Cardiovascular Diseases The objective of this study was to examine the association of 2 nonsynonymous in... BeFree 17962597 Detail
0.001 squamous cell carcinoma ICAM-1 rs5491 and rs281432 may be applied as factors to predict the clinical sta... BeFree 24069166 Detail
0.120 MALARIA, CEREBRAL, SUSCEPTIBILITY TO (finding) NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000201.3(ICAM1):c.167A>T (p.Lys56Met) AND Malaria, cerebral, susceptibility to ClinVar Detail
NM_000201.3(ICAM1):c.167A>T (p.Lys56Met) AND ICAM1-related disorder ClinVar Detail
The objective of this study was to examine the association of 2 nonsynonymous intercellular adhesion... DisGeNET Detail
ICAM-1 rs5491 and rs281432 may be applied as factors to predict the clinical stage in OSCC patients. DisGeNET Detail
NA 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
rs5491 dbSNP
Genome
hg38
Position
chr19:10,274,864-10,274,864
Variant Type
snv
Reference Allele
A
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
106.74
Standard deviation of sample read depth (HGVD)
52.79
Number of reference allele (HGVD)
2254
Number of alternative allele (HGVD)
166
Allele Frequency (HGVD)
0.06859504132231405
Gene Symbol (HGVD)
ICAM1
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))
rs5491
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0712
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1194
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)
483
East Asian Heterozygous Counts (ExAC)
465
East Asian Homozygous Counts (ExAC)
9
East Asian Allele Frequency (ExAC)
0.05585106382978723
Chromosome Counts in All Race (ExAC)
121346
Allele Counts in All Race (ExAC)
3758
Heterozygous Counts in All Race (ExAC)
3182
Homozygous Counts in All Race (ExAC)
288
Allele Frequency in All Race (ExAC)
0.030969294414319386
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