chr2:162267541:C>T Detail (hg38) (IFIH1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:163,124,051-163,124,051 View the variant detail on this assembly version. |
| hg38 | chr2:162,267,541-162,267,541 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | ||
| Ensemble | ENST00000648433.1:c.2719G>A | ENST00000648433.1:p.Ala907Thr |
| ENST00000649979.2:c.2836G>A | ENST00000649979.2:p.Ala946Thr |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.230 |
| ToMMo:0.230 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.174 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2023-11-12 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | Singleton-Merten syndrome 1,Aicardi-Goutieres syndrome 7 |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | Singleton-Merten syndrome 1,Aicardi-Goutieres syndrome 7 |
germline
|
Detail |
|
Benign
|
2018-11-12 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2021-08-10 | criteria provided, single submitter | Aicardi-Goutieres syndrome 7 |
germline
|
Detail |
|
Benign
|
2021-08-10 | criteria provided, single submitter | Singleton-Merten syndrome 1 |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.248 | Diabetes Mellitus, Insulin-Dependent | Evidence for association with T1D was observed for the IFIH1 SNP, rs1990760 (P=7... | BeFree | 19956106 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | Evidence for association with T1D was observed for the IFIH1 SNP, rs1990760 (P=7... | BeFree | 19956106 | Detail |
| 0.010 | Autoimmune Diseases | We confirm a significant contribution of the Ala946Thr IFIH1 polymorphism to org... | BeFree | 17535987 | Detail |
| 0.123 | Graves Disease | This meta-analysis demonstrates that the IFIH1 rs1990760 T-allele confers suscep... | BeFree | 23734776 | Detail |
| 0.208 | Lupus Erythematosus, Systemic | Association study of IFIH1 rs1990760 polymorphism with systemic lupus erythemato... | BeFree | 23108955 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | Robust associations of four new chromosome regions from genome-wide analyses of ... | GWASCAT | 17554260 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | In conclusion, IFIH1 rs3747517, but not rs1990760 polymorphism, plays an importa... | BeFree | 22053898 | Detail |
| <0.001 | rheumatoid arthritis | These results indicate that the IFIH1 is upregulated in RA but that the A946T va... | BeFree | 17442111 | Detail |
| 0.002 | Diabetes Mellitus, Non-Insulin-Dependent | [These results suggest that individuals with increased genetic susceptibility to... | GAD | 20203524 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | Moreover, the association of the Thr946Ala SNP with T1D is not due to modulation... | BeFree | 20644636 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | The rs1990760 polymorphism of interferon induced with helicase C domain 1 (IFIH1... | BeFree | 24386202 | Detail |
| <0.001 | Hypertensive disease | The A allele of the rs1990760 polymorphism in the IFIH1 gene is associated with ... | BeFree | 24386202 | Detail |
| 0.208 | Lupus Erythematosus, Systemic | In addition to the known association of HLA with IgAD, we identified association... | BeFree | 20694011 | Detail |
| 0.208 | Lupus Erythematosus, Systemic | Our study supports previous findings of an association between the rs1990760 pol... | BeFree | 24719229 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | Recent studies showed that a genetic variation within the interferon induced hel... | BeFree | 19961590 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | Enterovirus RNA in peripheral blood may be associated with the variants of rs199... | BeFree | 23144876 | Detail |
| 0.123 | Graves Disease | Therefore we were unable to find the association of A946T polymorphism of the IF... | BeFree | 18026693 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | The aim of the present study was to investigate the role of the interferon induc... | BeFree | 17442111 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | Functional characterization of the Thr946Ala SNP at the type 1 diabetes IFIH1 lo... | BeFree | 24117221 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | Genome-wide association study and meta-analysis find that over 40 loci affect ri... | GWASCAT | 19430480 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | The interferon-induced helicase IFIH1 Ala946Thr polymorphism is associated with ... | BeFree | 19841890 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | A recent large-scale analysis of nonsynonymous coding polymorphisms showed stron... | BeFree | 17535987 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | [Eleven of 52 non-MHC T1D loci showed evidence of association with at least one ... | GAD | 21829393 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | This meta-analysis demonstrates that the IFIH1 rs1990760 T-allele confers suscep... | BeFree | 23734776 | Detail |
| <0.001 | rheumatoid arthritis | This meta-analysis demonstrates that the IFIH1 rs1990760 T-allele confers suscep... | BeFree | 23734776 | Detail |
| 0.167 | Diabetes Mellitus, Insulin-Dependent | In addition to the known association of HLA with IgAD, we identified association... | BeFree | 20694011 | Detail |
| 0.010 | Autoimmune Diseases | Association of IFIH1 rs1990760 polymorphism with susceptibility to autoimmune di... | BeFree | 23734776 | Detail |
| 0.015 | melanoma | We investigated the association of polymorphisms in three pattern recognition re... | BeFree | 24621100 | Detail |
| 0.002 | melanoma | We investigated the association of polymorphisms in three pattern recognition re... | BeFree | 24621100 | Detail |
| 0.009 | melanoma | We investigated the association of polymorphisms in three pattern recognition re... | BeFree | 24621100 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_022168.4(IFIH1):c.2836G>A (p.Ala946Thr) AND not specified | ClinVar | Detail |
| NM_022168.4(IFIH1):c.2836G>A (p.Ala946Thr) AND multiple conditions | ClinVar | Detail |
| NM_022168.4(IFIH1):c.2836G>A (p.Ala946Thr) AND multiple conditions | ClinVar | Detail |
| NM_022168.4(IFIH1):c.2836G>A (p.Ala946Thr) AND not provided | ClinVar | Detail |
| NM_022168.4(IFIH1):c.2836G>A (p.Ala946Thr) AND Aicardi-Goutieres syndrome 7 | ClinVar | Detail |
| NM_022168.4(IFIH1):c.2836G>A (p.Ala946Thr) AND Singleton-Merten syndrome 1 | ClinVar | Detail |
| Evidence for association with T1D was observed for the IFIH1 SNP, rs1990760 (P=7.0 x 10(-4)), with R... | DisGeNET | Detail |
| Evidence for association with T1D was observed for the IFIH1 SNP, rs1990760 (P=7.0 x 10(-4)), with R... | DisGeNET | Detail |
| We confirm a significant contribution of the Ala946Thr IFIH1 polymorphism to organ-specific autoimmu... | DisGeNET | Detail |
| This meta-analysis demonstrates that the IFIH1 rs1990760 T-allele confers susceptibility to T1D, SLE... | DisGeNET | Detail |
| Association study of IFIH1 rs1990760 polymorphism with systemic lupus erythematosus in a Chinese pop... | DisGeNET | Detail |
| Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. | DisGeNET | Detail |
| In conclusion, IFIH1 rs3747517, but not rs1990760 polymorphism, plays an important role in type 1 di... | DisGeNET | Detail |
| These results indicate that the IFIH1 is upregulated in RA but that the A946T variant does not contr... | DisGeNET | Detail |
| [These results suggest that individuals with increased genetic susceptibility to T2D have decreased ... | DisGeNET | Detail |
| Moreover, the association of the Thr946Ala SNP with T1D is not due to modulation of IFIH1 expression... | DisGeNET | Detail |
| The rs1990760 polymorphism of interferon induced with helicase C domain 1 (IFIH1) has been associate... | DisGeNET | Detail |
| The A allele of the rs1990760 polymorphism in the IFIH1 gene is associated with protection for arter... | DisGeNET | Detail |
| In addition to the known association of HLA with IgAD, we identified association with a nonsynonymou... | DisGeNET | Detail |
| Our study supports previous findings of an association between the rs1990760 polymorphism of IFIH1 a... | DisGeNET | Detail |
| Recent studies showed that a genetic variation within the interferon induced helicase domain 1 (IFIH... | DisGeNET | Detail |
| Enterovirus RNA in peripheral blood may be associated with the variants of rs1990760, a common type ... | DisGeNET | Detail |
| Therefore we were unable to find the association of A946T polymorphism of the IFIH1 gene with the de... | DisGeNET | Detail |
| The aim of the present study was to investigate the role of the interferon induced with helicase dom... | DisGeNET | Detail |
| Functional characterization of the Thr946Ala SNP at the type 1 diabetes IFIH1 locus. | DisGeNET | Detail |
| Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabete... | DisGeNET | Detail |
| The interferon-induced helicase IFIH1 Ala946Thr polymorphism is associated with type 1 diabetes in b... | DisGeNET | Detail |
| A recent large-scale analysis of nonsynonymous coding polymorphisms showed strong evidence that an a... | DisGeNET | Detail |
| [Eleven of 52 non-MHC T1D loci showed evidence of association with at least one autoantibody at a fa... | DisGeNET | Detail |
| This meta-analysis demonstrates that the IFIH1 rs1990760 T-allele confers susceptibility to T1D, SLE... | DisGeNET | Detail |
| This meta-analysis demonstrates that the IFIH1 rs1990760 T-allele confers susceptibility to T1D, SLE... | DisGeNET | Detail |
| In addition to the known association of HLA with IgAD, we identified association with a nonsynonymou... | DisGeNET | Detail |
| Association of IFIH1 rs1990760 polymorphism with susceptibility to autoimmune diseases: a meta-analy... | DisGeNET | Detail |
| We investigated the association of polymorphisms in three pattern recognition receptor (PRR) genes-t... | DisGeNET | Detail |
| We investigated the association of polymorphisms in three pattern recognition receptor (PRR) genes-t... | DisGeNET | Detail |
| We investigated the association of polymorphisms in three pattern recognition receptor (PRR) genes-t... | 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
- rs1990760 dbSNP
- Genome
- hg38
- Position
- chr2:162,267,541-162,267,541
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1200
- Mean of sample read depth (HGVD)
- 126.81
- Standard deviation of sample read depth (HGVD)
- 57.27
- Number of reference allele (HGVD)
- 1848
- Number of alternative allele (HGVD)
- 551
- Allele Frequency (HGVD)
- 0.22967903293038766
- Gene Symbol (HGVD)
- IFIH1
- 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))
- rs1990760
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.2299
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 3853
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8652
- East Asian Allele Counts (ExAC)
- 1503
- East Asian Heterozygous Counts (ExAC)
- 1247
- East Asian Homozygous Counts (ExAC)
- 128
- East Asian Allele Frequency (ExAC)
- 0.17371705963938974
- Chromosome Counts in All Race (ExAC)
- 121342
- Allele Counts in All Race (ExAC)
- 61242
- Heterozygous Counts in All Race (ExAC)
- 27092
- Homozygous Counts in All Race (ExAC)
- 17075
- Allele Frequency in All Race (ExAC)
- 0.5047057078340558
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