chr17:50072022:C>T Detail (hg38) (ITGA3)

Information

Genome

Assembly Position
hg19 chr17:48,149,386-48,149,386 View the variant detail on this assembly version.
hg38 chr17:50,072,022-50,072,022

HGVS

Type Transcript Protein
RefSeq NM_002204.3:c.996C>T NP_002195.1:p.Phe332=
Ensemble ENST00000007722.11:c.996C>T ENST00000007722.11:p.Phe332=
ENST00000320031.13:c.996C>T ENST00000320031.13:p.Phe332=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.314
ToMMo:0.321
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.324

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605025 OMIM
HGNC 6139 HGNC
Ensembl ENSG00000005884 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv58040362 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.006 Neoplasm Metastasis The following factors resulted independently associated with peritoneal carcinos... BeFree 20926544 Detail
<0.001 Carcinomatosis Tumor histology represents a crucial issue conditioning tumoral behavior; genoty... BeFree 20926544 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002204.4(ITGA3):c.996C>T (p.Phe332=) AND not provided ClinVar Detail
The following factors resulted independently associated with peritoneal carcinosis or hematogenous m... DisGeNET Detail
Tumor histology represents a crucial issue conditioning tumoral behavior; genotyping of rs2269772 (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
-
dbSNP
rs2269772 dbSNP
Genome
hg38
Position
chr17:50,072,022-50,072,022
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1133
Mean of sample read depth (HGVD)
59.14
Standard deviation of sample read depth (HGVD)
27.74
Number of reference allele (HGVD)
1555
Number of alternative allele (HGVD)
711
Allele Frequency (HGVD)
0.3137687555163283
Gene Symbol (HGVD)
ITGA3
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))
rs2269772
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3209
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5379
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8626
East Asian Allele Counts (ExAC)
2798
East Asian Heterozygous Counts (ExAC)
1924
East Asian Homozygous Counts (ExAC)
437
East Asian Allele Frequency (ExAC)
0.3243681891954556
Chromosome Counts in All Race (ExAC)
120774
Allele Counts in All Race (ExAC)
20317
Heterozygous Counts in All Race (ExAC)
15871
Homozygous Counts in All Race (ExAC)
2223
Allele Frequency in All Race (ExAC)
0.16822329309288422
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