chr5:180619344:G>C Detail (hg38) (FLT4)

Information

Genome

Assembly Position
hg19 chr5:180,046,344-180,046,344 View the variant detail on this assembly version.
hg38 chr5:180,619,344-180,619,344

HGVS

Type Transcript Protein
RefSeq NM_182925.4:c.2670C>G NP_891555.2:p.His890Gln
NM_002020.4:c.2670C>G NP_002011.2:p.His890Gln
Ensemble ENST00000261937.11:c.2670C>G ENST00000261937.11:p.His890Gln
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.461
ToMMo:0.507
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.486

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 136352 OMIM
HGNC 3767 HGNC
Ensembl ENSG00000037280 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv23982458 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-29 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2018-11-11 criteria provided, single submitter not provided germline Detail
Benign 2021-08-10 criteria provided, single submitter Congenital heart defects, multiple types, 7 germline Detail
Benign 2021-08-10 criteria provided, single submitter Hereditary lymphedema type I germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Conventional (Clear Cell) Renal Cell Carcinoma Our results indicate that VEGFA rs2010963 and VEGFR3 rs448012 are associated wit... BeFree 25239121 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_182925.5(FLT4):c.2670C>G (p.His890Gln) AND not specified ClinVar Detail
NM_182925.5(FLT4):c.2670C>G (p.His890Gln) AND not provided ClinVar Detail
NM_182925.5(FLT4):c.2670C>G (p.His890Gln) AND Congenital heart defects, multiple types, 7 ClinVar Detail
NM_182925.5(FLT4):c.2670C>G (p.His890Gln) AND Hereditary lymphedema type I ClinVar Detail
Our results indicate that VEGFA rs2010963 and VEGFR3 rs448012 are associated with risk of ccRCC. 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
rs448012 dbSNP
Genome
hg38
Position
chr5:180,619,344-180,619,344
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1169
Mean of sample read depth (HGVD)
62.64
Standard deviation of sample read depth (HGVD)
31.46
Number of reference allele (HGVD)
1260
Number of alternative allele (HGVD)
1077
Allele Frequency (HGVD)
0.46084724005134786
Gene Symbol (HGVD)
FLT4
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))
rs448012
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5068
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8488
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16748
East Asian Chromosome Counts (ExAC)
8430
East Asian Allele Counts (ExAC)
4100
East Asian Heterozygous Counts (ExAC)
2106
East Asian Homozygous Counts (ExAC)
997
East Asian Allele Frequency (ExAC)
0.4863582443653618
Chromosome Counts in All Race (ExAC)
117612
Allele Counts in All Race (ExAC)
73477
Heterozygous Counts in All Race (ExAC)
26931
Homozygous Counts in All Race (ExAC)
23273
Allele Frequency in All Race (ExAC)
0.6247406727204707
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