chr20:44406053:C>T Detail (hg38) (HNF4A)

Information

Genome

Assembly Position
hg19 chr20:43,034,693-43,034,693 View the variant detail on this assembly version.
hg38 chr20:44,406,053-44,406,053

HGVS

Type Transcript Protein
RefSeq NM_000457.4:c.116-5C>T
NM_001258355.1:c.116-5C>T
NM_178849.2:c.116-5C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.198
ToMMo:0.193
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.176

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600281 OMIM
HGNC 5024 HGNC
Ensembl ENSG00000101076 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv63819669 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-04-24 criteria provided, multiple submitters, no conflicts not specified germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Hyperinsulinism, Dominant germline Detail
Benign Likely benign 2016-06-14 criteria provided, multiple submitters, no conflicts Maturity onset diabetes mellitus in young germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign criteria provided, single submitter somatic Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.374 Diabetes Mellitus, Non-Insulin-Dependent These results indicate that the associations of HNF4A rs1885088 with glucose tol... BeFree 19406499 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_175914.5(HNF4A):c.50-5C>T AND not specified ClinVar Detail
NM_175914.5(HNF4A):c.50-5C>T AND Hyperinsulinism, Dominant ClinVar Detail
NM_175914.5(HNF4A):c.50-5C>T AND Maturity onset diabetes mellitus in young ClinVar Detail
NM_175914.5(HNF4A):c.50-5C>T AND not provided ClinVar Detail
NM_175914.5(HNF4A):c.50-5C>T AND Glycosuria ClinVar Detail
These results indicate that the associations of HNF4A rs1885088 with glucose tolerance and rs745975 ... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs745975 dbSNP
Genome
hg38
Position
chr20:44,406,053-44,406,053
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
879
Mean of sample read depth (HGVD)
14.45
Standard deviation of sample read depth (HGVD)
31.67
Number of reference allele (HGVD)
1410
Number of alternative allele (HGVD)
348
Allele Frequency (HGVD)
0.19795221843003413
Gene Symbol (HGVD)
HNF4A
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))
rs745975
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1926
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3228
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8630
East Asian Allele Counts (ExAC)
1515
East Asian Heterozygous Counts (ExAC)
1265
East Asian Homozygous Counts (ExAC)
125
East Asian Allele Frequency (ExAC)
0.17555040556199306
Chromosome Counts in All Race (ExAC)
121188
Allele Counts in All Race (ExAC)
24333
Heterozygous Counts in All Race (ExAC)
18953
Homozygous Counts in All Race (ExAC)
2690
Allele Frequency in All Race (ExAC)
0.20078720665412417
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