chr12:120997784:G>T Detail (hg38) (HNF1A)

Information

Genome

Assembly Position
hg19 chr12:121,435,587-121,435,587 View the variant detail on this assembly version.
hg38 chr12:120,997,784-120,997,784

HGVS

Type Transcript Protein
RefSeq NM_000545.6:c.1501+119G>T
NM_001306179.1:c.1501+119G>T
Ensemble ENST00000257555.11:c.1501+119G>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.541
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.452

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 tgv47500727 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-24 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.008 coronary artery disease [We identified one new CAD risk locus on 3q22.3 in MRAS (P = 7.44 x 10(-13); OR ... GAD 19198612 Detail
0.003 coronary artery disease [We identified one new CAD risk locus on 3q22.3 in MRAS (P = 7.44 x 10(-13); OR ... GAD 19198612 Detail
0.003 Coronary Arteriosclerosis In the LURIC Study cohort the A-allele of rs2259816 is associated with decreased... BeFree 21062467 Detail
0.008 coronary artery disease Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of ... BeFree 21062467 Detail
0.127 Coronary heart disease Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of ... BeFree 21062467 Detail
0.001 Coronary Arteriosclerosis Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of ... BeFree 21062467 Detail
0.008 coronary artery disease [Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of... GAD 21062467 Detail
0.167 coronary artery disease Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of ... BeFree 21062467 Detail
0.127 Coronary heart disease New susceptibility locus for coronary artery disease on chromosome 3q22.3. GWASCAT 19198612 Detail
0.069 Coronary heart disease Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of ... BeFree 21062467 Detail
0.027 Coronary Arteriosclerosis Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of ... BeFree 21062467 Detail
0.005 Coronary heart disease In the LURIC Study cohort the A-allele of rs2259816 is associated with decreased... BeFree 21062467 Detail
0.004 coronary artery disease In the LURIC Study cohort the A-allele of rs2259816 is associated with decreased... BeFree 21062467 Detail
0.126 Coronary heart disease Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1... BeFree 22152955 Detail
0.025 Coronary heart disease Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1... BeFree 22152955 Detail
0.004 Coronary heart disease Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1... BeFree 22152955 Detail
0.128 Coronary heart disease Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1... BeFree 22152955 Detail
0.016 Coronary heart disease Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1... BeFree 22152955 Detail
0.127 Coronary heart disease Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1... BeFree 22152955 Detail
0.126 Coronary heart disease Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1... BeFree 22152955 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000545.8(HNF1A):c.1501+119G>T AND not provided ClinVar Detail
[We identified one new CAD risk locus on 3q22.3 in MRAS (P = 7.44 x 10(-13); OR = 1.15, 95% CI = 1.1... DisGeNET Detail
[We identified one new CAD risk locus on 3q22.3 in MRAS (P = 7.44 x 10(-13); OR = 1.15, 95% CI = 1.1... DisGeNET Detail
In the LURIC Study cohort the A-allele of rs2259816 is associated with decreased CRP but not with co... DisGeNET Detail
Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of c-reactive protein a... DisGeNET Detail
Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of c-reactive protein a... DisGeNET Detail
Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of c-reactive protein a... DisGeNET Detail
[Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of c-reactive protein ... DisGeNET Detail
Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of c-reactive protein a... DisGeNET Detail
New susceptibility locus for coronary artery disease on chromosome 3q22.3. DisGeNET Detail
Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of c-reactive protein a... DisGeNET Detail
Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of c-reactive protein a... DisGeNET Detail
In the LURIC Study cohort the A-allele of rs2259816 is associated with decreased CRP but not with co... DisGeNET Detail
In the LURIC Study cohort the A-allele of rs2259816 is associated with decreased CRP but not with co... DisGeNET Detail
Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1), rs646776 (CELSR2-... DisGeNET Detail
Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1), rs646776 (CELSR2-... DisGeNET Detail
Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1), rs646776 (CELSR2-... DisGeNET Detail
Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1), rs646776 (CELSR2-... DisGeNET Detail
Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1), rs646776 (CELSR2-... DisGeNET Detail
Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1), rs646776 (CELSR2-... DisGeNET Detail
Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1), rs646776 (CELSR2-... 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
rs2259816 dbSNP
Genome
hg38
Position
chr12:120,997,784-120,997,784
Variant Type
snv
Reference Allele
G
Alternative Allele
T
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))
rs2259816
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5414
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9073
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
568
East Asian Allele Counts (ExAC)
257
East Asian Heterozygous Counts (ExAC)
141
East Asian Homozygous Counts (ExAC)
58
East Asian Allele Frequency (ExAC)
0.4524647887323944
Chromosome Counts in All Race (ExAC)
16254
Allele Counts in All Race (ExAC)
7302
Heterozygous Counts in All Race (ExAC)
3866
Homozygous Counts in All Race (ExAC)
1718
Allele Frequency in All Race (ExAC)
0.44924326319675156
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