chr15:78789488:C>T Detail (hg19) (IREB2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr15:78,789,488-78,789,488 |
| hg38 | chr15:78,497,146-78,497,146 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001320941.1:c.2616C>T | NP_001307870.1:p.Ala872= |
| NM_001320942.1:c.2616C>T | NP_001307871.1:p.Ala872= | |
| NM_004136.3:c.2616C>T | NP_004127.1:p.Ala872= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.392 |
| ToMMo:0.392 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.475 |
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
|
2021-08-19 | criteria provided, single submitter | Neurodegeneration, early-onset, with choreoathetoid movements and microcytic anemia |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2019-10-30 | criteria provided, single submitter | IREB2-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.129 | Chronic Obstructive Airway Disease | [Variants in FAM13A are associated with chronic obstructive pulmonary disease.] | GAD | 20173748 | Detail |
| 0.127 | Chronic Obstructive Airway Disease | [Variants in FAM13A are associated with chronic obstructive pulmonary disease.] | GAD | 20173748 | Detail |
| 0.129 | Chronic Obstructive Airway Disease | Variants in FAM13A are associated with chronic obstructive pulmonary disease. | GWASCAT | 20173748 | Detail |
| 0.129 | Chronic Obstructive Airway Disease | Our results support that IREB2 rs13180 is associated with COPD in Hainan populat... | BeFree | 25565795 | Detail |
| 0.129 | Chronic Obstructive Airway Disease | [Variants in FAM13A are associated with chronic obstructive pulmonary disease.] | GAD | 20173748 | Detail |
| 0.003 | Chronic Obstructive Airway Disease | We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13... | BeFree | 22461431 | Detail |
| <0.001 | Chronic Obstructive Airway Disease | We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13... | BeFree | 22461431 | Detail |
| 0.248 | Chronic Obstructive Airway Disease | We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13... | BeFree | 22461431 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_004136.4(IREB2):c.2616C>T (p.Ala872=) AND Neurodegeneration, early-onset, with choreoathetoid mov... | ClinVar | Detail |
| NM_004136.4(IREB2):c.2616C>T (p.Ala872=) AND not provided | ClinVar | Detail |
| NM_004136.4(IREB2):c.2616C>T (p.Ala872=) AND IREB2-related disorder | ClinVar | Detail |
| [Variants in FAM13A are associated with chronic obstructive pulmonary disease.] | DisGeNET | Detail |
| [Variants in FAM13A are associated with chronic obstructive pulmonary disease.] | DisGeNET | Detail |
| Variants in FAM13A are associated with chronic obstructive pulmonary disease. | DisGeNET | Detail |
| Our results support that IREB2 rs13180 is associated with COPD in Hainan population. | DisGeNET | Detail |
| [Variants in FAM13A are associated with chronic obstructive pulmonary disease.] | DisGeNET | Detail |
| We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13180 (IREB2), and rs8... | DisGeNET | Detail |
| We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13180 (IREB2), and rs8... | DisGeNET | Detail |
| We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13180 (IREB2), and rs8... | 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
- rs13180 dbSNP
- Genome
- hg19
- Position
- chr15:78,789,488-78,789,488
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1163
- Mean of sample read depth (HGVD)
- 62.91
- Standard deviation of sample read depth (HGVD)
- 26.87
- Number of reference allele (HGVD)
- 1414
- Number of alternative allele (HGVD)
- 911
- Allele Frequency (HGVD)
- 0.39182795698924733
- Gene Symbol (HGVD)
- IREB2
- 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))
- rs13180
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.3916
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 6564
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8648
- East Asian Allele Counts (ExAC)
- 4111
- East Asian Heterozygous Counts (ExAC)
- 2111
- East Asian Homozygous Counts (ExAC)
- 1000
- East Asian Allele Frequency (ExAC)
- 0.4753700277520814
- Chromosome Counts in All Race (ExAC)
- 121306
- Allele Counts in All Race (ExAC)
- 65976
- Heterozygous Counts in All Race (ExAC)
- 28844
- Homozygous Counts in All Race (ExAC)
- 18566
- Allele Frequency in All Race (ExAC)
- 0.5438807643480125
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