chr17:40498565:T>C Detail (hg19) (STAT3)

Information

Genome

Assembly Position
hg19 chr17:40,498,565-40,498,565
hg38 chr17:42,346,547-42,346,547 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_213662.1:c.273+22A>G
NM_003150.3:c.273+22A>G
NM_139276.2:c.273+22A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.010
ToMMo:0.009
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.014

Prediction

ClinVar

Clinical Significance Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 102582 OMIM
HGNC 11364 HGNC
Ensembl ENSG00000168610 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57809824 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2020-05-30 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 thyroiditis We genotyped six single-nucleotide polymorphisms (SNPs) rs1053005, rs2293152, rs... BeFree 24081513 Detail
<0.001 Graves Disease We genotyped six single-nucleotide polymorphisms (SNPs) rs1053005, rs2293152, rs... BeFree 24081513 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_139276.3(STAT3):c.273+22A>G AND not provided ClinVar Detail
We genotyped six single-nucleotide polymorphisms (SNPs) rs1053005, rs2293152, rs744166, rs17593222, ... DisGeNET Detail
We genotyped six single-nucleotide polymorphisms (SNPs) rs1053005, rs2293152, rs744166, rs17593222, ... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2291282 dbSNP
Genome
hg19
Position
chr17:40,498,565-40,498,565
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
835
Mean of sample read depth (HGVD)
20.81
Standard deviation of sample read depth (HGVD)
29.55
Number of reference allele (HGVD)
1654
Number of alternative allele (HGVD)
16
Allele Frequency (HGVD)
0.009580838323353293
Gene Symbol (HGVD)
STAT3
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))
rs2291282
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0092
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
155
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
117
East Asian Heterozygous Counts (ExAC)
113
East Asian Homozygous Counts (ExAC)
2
East Asian Allele Frequency (ExAC)
0.013519759648717357
Chromosome Counts in All Race (ExAC)
121402
Allele Counts in All Race (ExAC)
124
Heterozygous Counts in All Race (ExAC)
120
Homozygous Counts in All Race (ExAC)
2
Allele Frequency in All Race (ExAC)
0.0010213999769361295
Genome browser