chr12:120997624:G>A Detail (hg38) (HNF1A)

Information

Genome

Assembly Position
hg19 chr12:121,435,427-121,435,427 View the variant detail on this assembly version.
hg38 chr12:120,997,624-120,997,624

HGVS

Type Transcript Protein
RefSeq NM_000545.6:c.1460G>A NP_000536.5:p.Ser487Asn
NM_001306179.1:c.1460G>A NP_001293108.1:p.Ser487Asn
Ensemble ENST00000257555.11:c.1460G>A ENST00000257555.11:p.Ser487Asn
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.551
ToMMo:0.544
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.500

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 142410 OMIM
HGNC 11621 HGNC
Ensembl ENSG00000135100 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv47500693 TogoVar
COSMIC COSM4984989 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2014-11-18 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-08-10 criteria provided, multiple submitters, no conflicts maturity-onset diabetes of the young type 3 germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign criteria provided, single submitter type 2 diabetes mellitus somatic Detail
Benign 2015-09-27 criteria provided, single submitter Maturity onset diabetes mellitus in young germline Detail
Benign 2023-07-07 criteria provided, single submitter nonpapillary renal cell carcinoma germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.007 Impaired glucose tolerance The common variants p.I27L (rs1169288), p.A98V (rs1800574) and p.S487N (rs246419... BeFree 24933231 Detail
0.127 Coronary heart disease The HNF1A Ser486Asn and/or Ile27Leu variants were also associated with increased... BeFree 20031592 Detail
0.001 Coronary Arteriosclerosis The HNF1A Ser486Asn and/or Ile27Leu variants were also associated with increased... BeFree 20031592 Detail
0.009 Inflammation NA GAD Detail
<0.001 Hypertensive disease The rs2259820_T (1.14 (1.03-1.26); P = 0.011) and rs2464196_C (1.12 (1.02-1.24);... BeFree 25057215 Detail
<0.001 Diabetes Mellitus, Non-Insulin-Dependent The rs2259820_T (1.14 (1.03-1.26); P = 0.011) and rs2464196_C (1.12 (1.02-1.24);... BeFree 25057215 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000545.8(HNF1A):c.1460G>A (p.Ser487Asn) AND not specified ClinVar Detail
NM_000545.8(HNF1A):c.1460G>A (p.Ser487Asn) AND Maturity-onset diabetes of the young type 3 ClinVar Detail
NM_000545.8(HNF1A):c.1460G>A (p.Ser487Asn) AND not provided ClinVar Detail
NM_000545.8(HNF1A):c.1460G>A (p.Ser487Asn) AND Type 2 diabetes mellitus ClinVar Detail
NM_000545.8(HNF1A):c.1460G>A (p.Ser487Asn) AND Maturity onset diabetes mellitus in young ClinVar Detail
NM_000545.8(HNF1A):c.1460G>A (p.Ser487Asn) AND Nonpapillary renal cell carcinoma ClinVar Detail
The common variants p.I27L (rs1169288), p.A98V (rs1800574) and p.S487N (rs2464196) of the hepatocyte... DisGeNET Detail
The HNF1A Ser486Asn and/or Ile27Leu variants were also associated with increased risk of subclinical... DisGeNET Detail
The HNF1A Ser486Asn and/or Ile27Leu variants were also associated with increased risk of subclinical... DisGeNET Detail
NA DisGeNET Detail
The rs2259820_T (1.14 (1.03-1.26); P = 0.011) and rs2464196_C (1.12 (1.02-1.24); P = 0.024) were ass... DisGeNET Detail
The rs2259820_T (1.14 (1.03-1.26); P = 0.011) and rs2464196_C (1.12 (1.02-1.24); P = 0.024) were ass... 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
rs2464196 dbSNP
Genome
hg38
Position
chr12:120,997,624-120,997,624
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Number of reference allele (HGVD)
1055
Number of alternative allele (HGVD)
1297
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1177
Mean of sample read depth (HGVD)
37.63
Standard deviation of sample read depth (HGVD)
18.05
Allele Frequency (HGVD)
0.5514455782312925
Gene Symbol (HGVD)
HNF1A
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))
rs2464196
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.544
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9117
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8188
East Asian Allele Counts (ExAC)
4093
East Asian Heterozygous Counts (ExAC)
2163
East Asian Homozygous Counts (ExAC)
965
East Asian Allele Frequency (ExAC)
0.4998778700537372
Chromosome Counts in All Race (ExAC)
112904
Allele Counts in All Race (ExAC)
39122
Heterozygous Counts in All Race (ExAC)
25544
Homozygous Counts in All Race (ExAC)
6789
Allele Frequency in All Race (ExAC)
0.3465067668107419
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