chr5:35871190:G>A Detail (hg19) (IL7R)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr5:35,871,190-35,871,190 |
hg38 | chr5:35,871,088-35,871,088 View the variant detail on this assembly version. |
HGVS
Type | Transcript | Protein |
---|---|---|
RefSeq | NM_002185.3:c.412G>A | NP_002176.2:p.Val138Ile |
Ensemble | ENST00000303115.8:c.412G>A | ENST00000303115.8:p.Val138Ile |
ENST00000506850.5:c.412G>A | ENST00000506850.5:p.Val138Ile |
Summary
MGeND
Clinical significance | |
Variant entry | |
GWAS entry | |
Disease area statistics | Show details |
Frequency
JP | HGVD:0.489 |
ToMMo:0.477 | |
NCBN:[No Data.] | |
NCBN(Hondo):[No Data.] | |
NCBN(Ryukyu):[No Data.] | |
East asia | ExAC:0.474 |
Prediction
ClinVar
Clinical Significance |
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Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
---|---|---|---|---|---|
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2024-01-23 | reviewed by expert panel | Immunodeficiency 104 |
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Detail |
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2024-01-24 | criteria provided, multiple submitters, no conflicts | not specified |
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Detail |
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2015-03-03 | criteria provided, single submitter | not provided |
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Detail |
CIViC
[No Data.]
DisGeNET
Score | Disease name | Description | Source | Pubmed | Links |
---|---|---|---|---|---|
0.004 | Lymphoma, Large-Cell, Follicular | A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... | BeFree | 20952689 | Detail |
0.003 | B-Cell Lymphomas | A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... | BeFree | 20952689 | Detail |
0.006 | Mucosa-Associated Lymphoid Tissue Lymphoma | After stratification by common B-cell lymphoma subtypes, a significant interacti... | BeFree | 20952689 | Detail |
0.050 | Lymphoma, Non-Hodgkin | A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... | BeFree | 20952689 | Detail |
0.021 | chronic lymphocytic leukemia | After stratification by common B-cell lymphoma subtypes, a significant interacti... | BeFree | 20952689 | Detail |
0.010 | B-Cell Lymphomas | A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... | BeFree | 20952689 | Detail |
0.004 | T-Cell Lymphoma | A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... | BeFree | 20952689 | Detail |
0.007 | Lymphoma, Follicular | After stratification by common B-cell lymphoma subtypes, a significant interacti... | BeFree | 20952689 | Detail |
0.002 | T-Cell Lymphoma | A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... | BeFree | 20952689 | Detail |
0.360 | Severe Combined Immunodeficiency, Autosomal Recessive, T Cell Negative, B Cell Positive, NK Cell Positive | NA | CLINVAR | Detail |
Annotation
Annotations
Descrption | Source | Links |
---|---|---|
NM_002185.5(IL7R):c.412G>A (p.Val138Ile) AND Immunodeficiency 104 | ClinVar | Detail |
NM_002185.5(IL7R):c.412G>A (p.Val138Ile) AND not specified | ClinVar | Detail |
NM_002185.5(IL7R):c.412G>A (p.Val138Ile) AND not provided | ClinVar | Detail |
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... | DisGeNET | Detail |
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... | DisGeNET | Detail |
After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for ... | DisGeNET | Detail |
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... | DisGeNET | Detail |
After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for ... | DisGeNET | Detail |
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... | DisGeNET | Detail |
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... | DisGeNET | Detail |
After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for ... | DisGeNET | Detail |
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... | DisGeNET | Detail |
NA | 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
- rs1494555 dbSNP
- Genome
- hg19
- Position
- chr5:35,871,190-35,871,190
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1188
- Mean of sample read depth (HGVD)
- 30.65
- Standard deviation of sample read depth (HGVD)
- 16.31
- Number of reference allele (HGVD)
- 1214
- Number of alternative allele (HGVD)
- 1162
- Allele Frequency (HGVD)
- 0.4890572390572391
- Gene Symbol (HGVD)
- IL7R
- 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))
- rs1494555
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4771
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 7996
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8642
- East Asian Allele Counts (ExAC)
- 4097
- East Asian Heterozygous Counts (ExAC)
- 2165
- East Asian Homozygous Counts (ExAC)
- 966
- East Asian Allele Frequency (ExAC)
- 0.47408007405693126
- Chromosome Counts in All Race (ExAC)
- 121272
- Allele Counts in All Race (ExAC)
- 79061
- Heterozygous Counts in All Race (ExAC)
- 25959
- Homozygous Counts in All Race (ExAC)
- 26551
- Allele Frequency in All Race (ExAC)
- 0.6519311959891814
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