chr20:44413724:C>T Detail (hg38) (HNF4A)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

Assembly	Position
hg19	chr20:43,042,364-43,042,364 View the variant detail on this assembly version.
hg38	chr20:44,413,724-44,413,724

HGVS

HNF4A

Type	Transcript	Protein
RefSeq	NM_000457.4:c.416C>T	NP_000448.3:p.Thr139Ile
	NM_001258355.1:c.416C>T	NP_001245284.1:p.Thr139Ile
	NM_178849.2:c.416C>T	NP_849180.1:p.Thr139Ile
	NM_178850.2:c.416C>T	NP_849181.1:p.Thr139Ile
	NM_001030003.2:c.350C>T	NP_001025174.1:p.Thr117Ile
	NM_175914.4:c.350C>T	NP_787110.2:p.Thr117Ile
	NM_001030004.2:c.350C>T	NP_001025175.1:p.Thr117Ile
	NM_001287184.1:c.350C>T	NP_001274113.1:p.Thr117Ile
Ensemble	ENST00000316099.10:c.416C>T	ENST00000316099.10:p.Thr139Ile
	ENST00000316673.9:c.350C>T	ENST00000316673.9:p.Thr117Ile
	ENST00000415691.2:c.416C>T	ENST00000415691.2:p.Thr139Ile
	ENST00000443598.6:c.416C>T	ENST00000443598.6:p.Thr139Ile
	ENST00000457232.5:c.350C>T	ENST00000457232.5:p.Thr117Ile
	ENST00000609795.5:c.350C>T	ENST00000609795.5:p.Thr117Ile

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.013
	ToMMo:0.009
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.013

Prediction

ClinVar

Clinical Significance	Benign Likely benign
Review star
Show details

Links

HNF4A

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	tgv63819977	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign Likely benign	2016-03-28	criteria provided, multiple submitters, no conflicts	not specified	germline	Detail
Likely benign	2017-04-27	criteria provided, single submitter	Familial hyperinsulinism	germline	Detail
Likely benign	2017-04-27	criteria provided, single submitter	maturity-onset diabetes of the young type 1	germline	Detail
Benign	2019-01-25	criteria provided, single submitter	Monogenic diabetes	unknown	Detail
Benign	2024-01-31	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail
Benign		criteria provided, single submitter	type 2 diabetes mellitus	somatic	Detail
Benign	2015-07-16	criteria provided, single submitter	Maturity onset diabetes mellitus in young	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.340	Diabetes Mellitus, Non-Insulin-Dependent	Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (H...	BeFree	25839936	Detail
0.614	Diabetes Mellitus, Non-Insulin-Dependent	Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (H...	BeFree	25839936	Detail
0.466	Diabetes Mellitus, Non-Insulin-Dependent	Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (H...	BeFree	25839936	Detail
0.055	Diabetes Mellitus, Non-Insulin-Dependent	Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (H...	BeFree	25839936	Detail
0.042	Diabetes Mellitus, Non-Insulin-Dependent	Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (H...	BeFree	25839936	Detail
0.121	Diabetes Mellitus, Non-Insulin-Dependent	Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (H...	BeFree	25839936	Detail
0.090	Diabetes Mellitus, Non-Insulin-Dependent	Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (H...	BeFree	25839936	Detail
0.025	Diabetes Mellitus, Non-Insulin-Dependent	Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (H...	BeFree	25839936	Detail

Annotation

Annotations

Descrption	Source	Links
NM_175914.5(HNF4A):c.350C>T (p.Thr117Ile) AND not specified	ClinVar	Detail
NM_175914.5(HNF4A):c.350C>T (p.Thr117Ile) AND Familial hyperinsulinism	ClinVar	Detail
NM_175914.5(HNF4A):c.350C>T (p.Thr117Ile) AND Maturity-onset diabetes of the young type 1	ClinVar	Detail
NM_175914.5(HNF4A):c.350C>T (p.Thr117Ile) AND Monogenic diabetes	ClinVar	Detail
NM_175914.5(HNF4A):c.350C>T (p.Thr117Ile) AND not provided	ClinVar	Detail
NM_175914.5(HNF4A):c.350C>T (p.Thr117Ile) AND Type 2 diabetes mellitus	ClinVar	Detail
NM_175914.5(HNF4A):c.350C>T (p.Thr117Ile) AND Maturity onset diabetes mellitus in young	ClinVar	Detail
Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (HNF4α), rs5219 (KCNJ1...	DisGeNET	Detail
Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (HNF4α), rs5219 (KCNJ1...	DisGeNET	Detail
Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (HNF4α), rs5219 (KCNJ1...	DisGeNET	Detail
Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (HNF4α), rs5219 (KCNJ1...	DisGeNET	Detail
Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (HNF4α), rs5219 (KCNJ1...	DisGeNET	Detail
Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (HNF4α), rs5219 (KCNJ1...	DisGeNET	Detail
Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (HNF4α), rs5219 (KCNJ1...	DisGeNET	Detail
Thus, we aimed to investigate the contribution of rs1111875 (HHEX), rs1800961 (HNF4α), rs5219 (KCNJ1...	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: rs1800961 dbSNP
Genome: hg38
Position: chr20:44,413,724-44,413,724
Variant Type: snv
Reference Allele: C
Alternative Allele: T
Filtering Status (HGVD): PASS
# of samples (HGVD): 1210
Mean of sample read depth (HGVD): 192.29
Standard deviation of sample read depth (HGVD): 91.35
Number of reference allele (HGVD): 2389
Number of alternative allele (HGVD): 31
Allele Frequency (HGVD): 0.0128099173553719
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)): rs1800961
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.0087
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 145
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16758
East Asian Chromosome Counts (ExAC): 8536
East Asian Allele Counts (ExAC): 114
East Asian Heterozygous Counts (ExAC): 108
East Asian Homozygous Counts (ExAC): 3
East Asian Allele Frequency (ExAC): 0.013355201499531396
Chromosome Counts in All Race (ExAC): 117108
Allele Counts in All Race (ExAC): 3748
Heterozygous Counts in All Race (ExAC): 3602
Homozygous Counts in All Race (ExAC): 73
Allele Frequency in All Race (ExAC): 0.03200464528469447

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