chr4:6291188:A>G Detail (hg38) (WFS1)

Information

Genome

Assembly Position
hg19 chr4:6,292,915-6,292,915 View the variant detail on this assembly version.
hg38 chr4:6,291,188-6,291,188

HGVS

Type Transcript Protein
RefSeq NM_001145853.1:c.461-9A>G
NM_006005.3:c.461-9A>G
Ensemble ENST00000226760.5:c.461-9A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.980
ToMMo:0.986
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.935

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606201 OMIM
HGNC 12762 HGNC
Ensembl ENSG00000109501 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv15957440 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2024-03-06 no assertion criteria provided type 2 diabetes mellitus germline Detail
Benign 2014-08-04 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2018-01-12 criteria provided, single submitter WFS1-Related Spectrum Disorders germline Detail
Benign 2018-01-12 criteria provided, single submitter Autosomal dominant nonsyndromic hearing loss 6 germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2020-11-20 criteria provided, multiple submitters, no conflicts Wolfram syndrome 1 germline unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.012 hyperglycemia Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO... BeFree 18853134 Detail
0.003 hyperglycemia Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO... BeFree 18853134 Detail
0.327 Diabetes Mellitus, Non-Insulin-Dependent A total of 1,578 non-diabetic individuals (534 men and 1,044 women, aged 40 +/- ... BeFree 19330314 Detail
0.327 Diabetes Mellitus, Non-Insulin-Dependent All the risk alleles in the 11 examined type 2 diabetes risk variants showed an ... BeFree 18984664 Detail
0.327 Diabetes Mellitus, Non-Insulin-Dependent Association of rs734312 and rs10010131 polymorphisms in WFS1 gene with type 2 di... BeFree 23257691 Detail
0.030 obesity Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO... BeFree 18853134 Detail
<0.001 gestational diabetes All the risk alleles in the 11 examined type 2 diabetes risk variants showed an ... BeFree 18984664 Detail
0.327 Diabetes Mellitus, Non-Insulin-Dependent While FTO rs8050136 and rs17817449, ADAMTS9 rs4607103, and WFS1 rs10010131 were ... BeFree 24145053 Detail
<0.001 hyperglycemia Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO... BeFree 18853134 Detail
0.129 Metabolic syndrome X Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO... BeFree 18853134 Detail
0.327 Diabetes Mellitus, Non-Insulin-Dependent A WFS1 haplotype consisting of the minor alleles of rs752854, rs10010131, and rs... BeFree 21713316 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_006005.3(WFS1):c.461-9A>G AND Type 2 diabetes mellitus ClinVar Detail
NM_006005.3(WFS1):c.461-9A>G AND not specified ClinVar Detail
NM_006005.3(WFS1):c.461-9A>G AND WFS1-Related Spectrum Disorders ClinVar Detail
NM_006005.3(WFS1):c.461-9A>G AND Autosomal dominant nonsyndromic hearing loss 6 ClinVar Detail
NM_006005.3(WFS1):c.461-9A>G AND not provided ClinVar Detail
NM_006005.3(WFS1):c.461-9A>G AND Wolfram syndrome 1 ClinVar Detail
Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO (rs9939609, OR 1.08... DisGeNET Detail
Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO (rs9939609, OR 1.08... DisGeNET Detail
A total of 1,578 non-diabetic individuals (534 men and 1,044 women, aged 40 +/- 13 years, BMI 28.9 +... DisGeNET Detail
All the risk alleles in the 11 examined type 2 diabetes risk variants showed an odds ratio (OR) grea... DisGeNET Detail
Association of rs734312 and rs10010131 polymorphisms in WFS1 gene with type 2 diabetes mellitus: a m... DisGeNET Detail
Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO (rs9939609, OR 1.08... DisGeNET Detail
All the risk alleles in the 11 examined type 2 diabetes risk variants showed an odds ratio (OR) grea... DisGeNET Detail
While FTO rs8050136 and rs17817449, ADAMTS9 rs4607103, and WFS1 rs10010131 were initially associated... DisGeNET Detail
Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO (rs9939609, OR 1.08... DisGeNET Detail
Polymorphisms in TCF7L2 (rs7903146, OR 1.10, 95% CI 1.04-1.17, p = 0.00097), FTO (rs9939609, OR 1.08... DisGeNET Detail
A WFS1 haplotype consisting of the minor alleles of rs752854, rs10010131, and rs734312 shows a prote... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs10010131 dbSNP
Genome
hg38
Position
chr4:6,291,188-6,291,188
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
64.06
Standard deviation of sample read depth (HGVD)
30.55
Number of reference allele (HGVD)
49
Number of alternative allele (HGVD)
2369
Allele Frequency (HGVD)
0.9797353184449958
Gene Symbol (HGVD)
WFS1
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))
rs10010131
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9861
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16527
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8600
East Asian Allele Counts (ExAC)
8039
East Asian Heterozygous Counts (ExAC)
521
East Asian Homozygous Counts (ExAC)
3759
East Asian Allele Frequency (ExAC)
0.9347674418604651
Chromosome Counts in All Race (ExAC)
120192
Allele Counts in All Race (ExAC)
78781
Heterozygous Counts in All Race (ExAC)
26219
Homozygous Counts in All Race (ExAC)
26281
Allele Frequency in All Race (ExAC)
0.6554595979765708
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