chr4:122826931:C>T Detail (hg38) (FGF2)

Information

Genome

Assembly Position
hg19 chr4:123,748,086-123,748,086 View the variant detail on this assembly version.
hg38 chr4:122,826,931-122,826,931

HGVS

Type Transcript Protein
RefSeq NM_002006.4:c.156C>T NP_001997.5:p.Ser52=
Ensemble ENST00000264498.9:c.156C>T ENST00000264498.9:p.Ser52=
ENST00000608478.1:c.-244C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.138
ToMMo:0.127
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.248

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 134920 OMIM
HGNC 3676 HGNC
Ensembl ENSG00000138685 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv18501365 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
0.002 breast carcinoma Here, we selected four commonly studied polymorphisms in VEGF, rs3025039 (known ... BeFree 22315135 Detail
0.002 Malignant neoplasm of breast Here, we selected four commonly studied polymorphisms in VEGF, rs3025039 (known ... BeFree 22315135 Detail
Annotation

Annotations

DescrptionSourceLinks
Here, we selected four commonly studied polymorphisms in VEGF, rs3025039 (known as +936 C/T), rs1109... DisGeNET Detail
Here, we selected four commonly studied polymorphisms in VEGF, rs3025039 (known as +936 C/T), rs1109... 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
hg38
Position
chr4:122,826,931-122,826,931
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
913
Mean of sample read depth (HGVD)
19.24
Standard deviation of sample read depth (HGVD)
10.20
Number of reference allele (HGVD)
1574
Number of alternative allele (HGVD)
252
Allele Frequency (HGVD)
0.1380065717415115
Gene Symbol (HGVD)
FGF2
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))
rs1449683
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1271
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2129
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
East Asian Chromosome Counts (ExAC)
1938
East Asian Allele Counts (ExAC)
481
East Asian Heterozygous Counts (ExAC)
413
East Asian Homozygous Counts (ExAC)
34
East Asian Allele Frequency (ExAC)
0.24819401444788441
Chromosome Counts in All Race (ExAC)
25784
Allele Counts in All Race (ExAC)
5517
Heterozygous Counts in All Race (ExAC)
4769
Homozygous Counts in All Race (ExAC)
374
Allele Frequency in All Race (ExAC)
0.2139699038163202
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