chr7:45893001:C>T Detail (hg38) (IGFBP1)

Information

Genome

Assembly Position
hg19 chr7:45,932,600-45,932,600 View the variant detail on this assembly version.
hg38 chr7:45,893,001-45,893,001

HGVS

Type Transcript Protein
RefSeq NM_000596.2:c.690C>T NP_000587.1:p.Cys230=
Ensemble ENST00000275525.8:c.690C>T ENST00000275525.8:p.Cys230=
ENST00000457280.5:c.684C>T ENST00000457280.5:p.Cys228=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.004
ToMMo:0.002
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.004

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 146730 OMIM
HGNC 5469 HGNC
Ensembl ENSG00000146678 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv29144007 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 ovary When evaluated individually, three SNPs in the IGFBPs (rs10228265, rs4988515 and... BeFree 19858071 Detail
0.001 ovarian carcinoma When evaluated individually, three SNPs in the IGFBPs (rs10228265, rs4988515 and... BeFree 19858071 Detail
Annotation

Annotations

DescrptionSourceLinks
When evaluated individually, three SNPs in the IGFBPs (rs10228265, rs4988515 and rs2270628) were ass... DisGeNET Detail
When evaluated individually, three SNPs in the IGFBPs (rs10228265, rs4988515 and rs2270628) were ass... 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
chr7:45,893,001-45,893,001
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
940
Mean of sample read depth (HGVD)
20.67
Standard deviation of sample read depth (HGVD)
13.83
Number of reference allele (HGVD)
1873
Number of alternative allele (HGVD)
7
Allele Frequency (HGVD)
0.003723404255319149
Gene Symbol (HGVD)
IGFBP1
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))
rs4988515
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0023
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
39
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
33
East Asian Heterozygous Counts (ExAC)
33
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0038141470180305132
Chromosome Counts in All Race (ExAC)
121360
Allele Counts in All Race (ExAC)
7892
Heterozygous Counts in All Race (ExAC)
7070
Homozygous Counts in All Race (ExAC)
411
Allele Frequency in All Race (ExAC)
0.06502966381015161
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