chr15:99478225:G>A Detail (hg19) (IGF1R)

Information

Genome

Assembly Position
hg19 chr15:99,478,225-99,478,225
hg38 chr15:98,934,996-98,934,996 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000649865.1:c.3126G>A ENST00000649865.1:p.Glu1042=
ENST00000650285.1:c.3129G>A ENST00000650285.1:p.Glu1043=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.273
ToMMo:0.269
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.353

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 147370 OMIM
HGNC 5465 HGNC
Ensembl ENSG00000140443 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv54164602 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2014-11-17 criteria provided, single submitter not specified germline Detail
Benign 2018-03-06 criteria provided, single submitter Growth delay due to insulin-like growth factor I resistance germline Detail
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Polyp of large intestine We examined the risk of colorectal polyps in relation to body size factors and c... BeFree 20580999 Detail
<0.001 Polyp of large intestine We examined the risk of colorectal polyps in relation to body size factors and c... BeFree 20580999 Detail
0.028 Malignant neoplasm of breast [Common genetic variation in candidate genes and susceptibility to subtypes of b... GAD 19124506 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000875.5(IGF1R):c.3129G>A (p.Glu1043=) AND not specified ClinVar Detail
NM_000875.5(IGF1R):c.3129G>A (p.Glu1043=) AND Growth delay due to insulin-like growth factor I resis... ClinVar Detail
NM_000875.5(IGF1R):c.3129G>A (p.Glu1043=) AND not provided ClinVar Detail
We examined the risk of colorectal polyps in relation to body size factors and candidate polymorphis... DisGeNET Detail
We examined the risk of colorectal polyps in relation to body size factors and candidate polymorphis... DisGeNET Detail
[Common genetic variation in candidate genes and susceptibility to subtypes of breast cancer.] 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
rs2229765 dbSNP
Genome
hg19
Position
chr15:99,478,225-99,478,225
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1201
Mean of sample read depth (HGVD)
91.25
Standard deviation of sample read depth (HGVD)
38.45
Number of reference allele (HGVD)
1746
Number of alternative allele (HGVD)
656
Allele Frequency (HGVD)
0.27310574521232306
Gene Symbol (HGVD)
IGF1R
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))
rs2229765
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2689
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4507
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8634
East Asian Allele Counts (ExAC)
3045
East Asian Heterozygous Counts (ExAC)
2005
East Asian Homozygous Counts (ExAC)
520
East Asian Allele Frequency (ExAC)
0.35267546907574704
Chromosome Counts in All Race (ExAC)
121316
Allele Counts in All Race (ExAC)
48186
Heterozygous Counts in All Race (ExAC)
28118
Homozygous Counts in All Race (ExAC)
10034
Allele Frequency in All Race (ExAC)
0.397194104652313
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