chr13:28624294:G>A Detail (hg19) (FLT3)

Information

Genome

Assembly Position
hg19 chr13:28,624,294-28,624,294
hg38 chr13:28,050,157-28,050,157 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_004119.2:c.680C>T NP_004110.2:p.Thr227Met
Ensemble ENST00000241453.12:c.680C>T ENST00000241453.12:p.Thr227Met
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.751
ToMMo:0.764
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.767

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 136351 OMIM
HGNC 3765 HGNC
Ensembl ENSG00000122025 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv48108419 TogoVar
COSMIC COSM5019176 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
not provided 2013-09-19 no assertion provided not specified germline Detail
Benign 2018-11-11 criteria provided, single submitter not provided germline Detail
CIViC
Disease Drug EL ET ED CS VO TR Pubmed Links
renal cell carcinoma Sunitinib B Predictive Supports Adverse Response Common Germline 3 19667267 Detail
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
In 219 patients with mostly Renal Cell Carcinoma and some Gastrointestinal Stromal tumors given suni... CIViC Evidence Detail
NM_004119.3(FLT3):c.680C>T (p.Thr227Met) AND not specified ClinVar Detail
NM_004119.3(FLT3):c.680C>T (p.Thr227Met) AND not provided ClinVar 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
rs1933437 dbSNP
Genome
hg19
Position
chr13:28,624,294-28,624,294
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
160.94
Standard deviation of sample read depth (HGVD)
68.84
Number of reference allele (HGVD)
602
Number of alternative allele (HGVD)
1818
Allele Frequency (HGVD)
0.7512396694214876
Gene Symbol (HGVD)
FLT3
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))
rs1933437
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7638
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12801
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
6629
East Asian Heterozygous Counts (ExAC)
1551
East Asian Homozygous Counts (ExAC)
2539
East Asian Allele Frequency (ExAC)
0.7668903285515964
Chromosome Counts in All Race (ExAC)
121366
Allele Counts in All Race (ExAC)
72671
Heterozygous Counts in All Race (ExAC)
27915
Homozygous Counts in All Race (ExAC)
22378
Allele Frequency in All Race (ExAC)
0.598775604370252
Variant (CIViC) (CIViC Variant)
T227M
Transcript 1 (CIViC Variant)
ENST00000241453.7
Variant URL (CIViC Variant)
https://civic.genome.wustl.edu/links/variants/540
Summary (CIViC Variant)
FLT3 T227M (rs1933437) is a common polymorphism with a GMAF around .60 based on the Exome Aggregation Consortium (ExAC) data. Its role in cancer predisposition is still unknown, however it may be associated with the development of leukopenia in patients treated with sunitinib.
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