chr19:10402938:G>A Detail (hg19) (ICAM5)

Information

Genome

Assembly Position
hg19 chr19:10,402,938-10,402,938
hg38 chr19:10,292,262-10,292,262 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_003259.3:c.901G>A NP_003250.3:p.Val301Ile
Ensemble ENST00000221980.5:c.901G>A ENST00000221980.5:p.Val301Ile
ENST00000586480.1:c.526G>A ENST00000586480.1:p.Val176Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.319
ToMMo:0.327
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.250

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 601852 OMIM
HGNC 5348 HGNC
Ensembl ENSG00000105376 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv61160942 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 Malignant neoplasm of breast Our meta-analysis suggests that the ICAM5 V301I and rs281439 variants but not IC... BeFree 23079714 Detail
0.006 Malignant neoplasm of breast Our meta-analysis suggests that the ICAM5 V301I and rs281439 variants but not IC... BeFree 23079714 Detail
<0.001 breast carcinoma Our meta-analysis suggests that the ICAM5 V301I and rs281439 variants but not IC... BeFree 23079714 Detail
0.004 breast carcinoma Our meta-analysis suggests that the ICAM5 V301I and rs281439 variants but not IC... BeFree 23079714 Detail
Annotation

Annotations

DescrptionSourceLinks
Our meta-analysis suggests that the ICAM5 V301I and rs281439 variants but not ICAM1 K469E polymorphi... DisGeNET Detail
Our meta-analysis suggests that the ICAM5 V301I and rs281439 variants but not ICAM1 K469E polymorphi... DisGeNET Detail
Our meta-analysis suggests that the ICAM5 V301I and rs281439 variants but not ICAM1 K469E polymorphi... DisGeNET Detail
Our meta-analysis suggests that the ICAM5 V301I and rs281439 variants but not ICAM1 K469E polymorphi... 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
hg19
Position
chr19:10,402,938-10,402,938
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1119
Mean of sample read depth (HGVD)
35.49
Standard deviation of sample read depth (HGVD)
16.59
Number of reference allele (HGVD)
1523
Number of alternative allele (HGVD)
715
Allele Frequency (HGVD)
0.3194816800714924
Gene Symbol (HGVD)
ICAM5
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))
rs1056538
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3274
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5486
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8264
East Asian Allele Counts (ExAC)
2065
East Asian Heterozygous Counts (ExAC)
1603
East Asian Homozygous Counts (ExAC)
231
East Asian Allele Frequency (ExAC)
0.24987899322362053
Chromosome Counts in All Race (ExAC)
116352
Allele Counts in All Race (ExAC)
44549
Heterozygous Counts in All Race (ExAC)
26273
Homozygous Counts in All Race (ExAC)
9138
Allele Frequency in All Race (ExAC)
0.3828812568756876
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