Summary
On this page, we'll dive into the Summary endpoint you can use to fetch summary statistics for genes and regions programmatically.
The summary model
The summary model contains all the statistics information about a gene or a region.
Properties
- Name
total- Type
- int
- Description
The total number of objects in the database
- Name
Common- Type
- Int
- Description
The number of objects with bravo_af > 0.01
- Name
Lowfreq- Type
- Int
- Description
The number of objects with bravo_af >= 0.0001 AND bravo_af < 0.01
- Name
Rare- Type
- Int
- Description
The number of rare objects with bravo_af < 0.0001
- Name
Singletons- Type
- Int
- Description
The number of objects with bravo_ac = 1
- Name
Doubletons- Type
- Int
- Description
The number of objects with bravo_ac = 2
- Name
Exonic- Type
- Int
- Description
The number of objects with genecode_comprehensive_category = 'exonic'
- Name
Utr- Type
- Int
- Description
The number of objects with genecode_comprehensive_category = 'UTR'
- Name
Ncrna- Type
- Int
- Description
The number of objects with genecode_comprehensive_category = 'ncRNA'
- Name
Intronic- Type
- Int
- Description
The number of objects with genecode_comprehensive_category = 'intronic'
- Name
Downstream- Type
- Int
- Description
The number of objects with genecode_comprehensive_category = 'downstream'
- Name
Intergenic- Type
- Int
- Description
The number of objects with genecode_comprehensive_category = 'intergenic'
- Name
Upstream- Type
- Int
- Description
The number of objects with genecode_comprehensive_category = 'upstream'
- Name
Splicing- Type
- Int
- Description
The number of objects with genecode_comprehensive_category = 'splicing'
- Name
Drugresponse- Type
- Int
- Description
The number of objects with clinical significance in ('drug_response', 'drug_response,_other', 'drug_response,_protective,_risk_factor')
- Name
Pathogenic- Type
- Int
- Description
The number of objects with clinical significance in ('Pathogenic,_Affects', 'Pathogenic,_protective', 'Pathogenic,_risk_factor', 'Pathogenic,_association', 'Pathogenic,_other', 'Pathogenic', 'Pathogenic,_drug_response','Pathogenic,_association,_protective')
- Name
Likelypathogenic- Type
- Int
- Description
The number of objects with clinical significance in ('Pathogenic/Likely_pathogenic,_risk_factor', 'Pathogenic/Likely_pathogenic,_other', 'Pathogenic/Likely_pathogenic', 'Likely_pathogenic,_association', 'Likely_pathogenic,_risk_factor', 'Pathogenic/Likely_pathogenic,_drug_response', 'Likely_pathogenic,_other,_risk_factor', 'association,_risk_factor', 'Likely_pathogenic')
- Name
Benign- Type
- Int
- Description
The number of objects with clinical significance in ('Benign', 'Benign,_risk_factor','protective','Benign,_other','Benign,_association')
- Name
Likelybenign- Type
- Int
- Description
The number of objects with clinical significance in ('Benign/Likely_benign', 'Likely_benign,_other', 'Benign/Likely_benign,_other', 'Likely_benign,_drug_response', 'Likely_benign','Benign/Likely_benign,_risk_factor')
- Name
Conflicting- Type
- Int
- Description
The number of objects with clinical significance in ('Conflicting_interpretations_of_pathogenicity', 'Conflicting_interpretations_of_pathogenicity,_other', 'Conflicting_interpretations_of_pathogenicity,_risk_factor', 'Conflicting_interpretations_of_pathogenicity,_protective', 'Conflicting_interpretations_of_pathogenicity,_Affects')
- Name
Unknown- Type
- Int
- Description
The number of objects with clinical significance in ('Uncertain_significance,_other', 'association', 'Uncertain_significance,_risk_factor', 'Uncertain_significance,_association', 'Uncertain_significance', 'Benign,_drug_response', 'association_not_found', 'Affects', 'other', 'Affects,_association', 'not_provided')
- Name
Plof- Type
- Int
- Description
The number of objects with genecode_comprehensive_exonic_category in ('stopgain', 'stoploss', 'frameshift deletion', 'frameshift insertion', 'splicing')
- Name
Nonsynonymous- Type
- Int
- Description
The number of objects with genecode_comprehensive_exonic_category = 'nonsynonymous SNV'
- Name
Synonymous- Type
- Int
- Description
The number of objects with genecode_comprehensive_exonic_category = 'synonymous SNV'
- Name
Deleterious- Type
- Int
- Description
The number of objects with sift_cat = 'deleterious'
- Name
Damaging- Type
- Int
- Description
The number of objects with polyphen_cat in ('probably_damaging', 'possibly_damaging')
- Name
Cageenhancer- Type
- Int
- Description
The number of objects with cage enhancer activity
- Name
Cagepromoter- Type
- Int
- Description
The number of objects with cage promoter activity
- Name
Apcproteinfunction- Type
- Int
- Description
The number of objects with APC protein function >= 10
- Name
Apcconservation- Type
- Int
- Description
The number of objects with APC conservation >= 10
- Name
Apcepigeneticsactive- Type
- Int
- Description
The number of objects with active APC epigenetics >= 10
- Name
Apcepigeneticsrepressive- Type
- Int
- Description
The number of objects with repressive APC epigenetics >= 10
- Name
Apcepigeneticstranscription- Type
- Int
- Description
The number of objects with APC epigenetics transcription >= 10
- Name
Apclocalnucleotidediversity- Type
- Int
- Description
The number of objects with local nucleotide diversity in APC >= 10
- Name
Apcmutationdensity- Type
- Int
- Description
The number of objects with mutation density in APC >= 10
- Name
Apctranscriptionfactor- Type
- Int
- Description
The number of objects with APC transcription factor >= 10
- Name
Apcmappability- Type
- Int
- Description
The number of objects with APC mappability >= 10
- Name
Caddphred- Type
- Int
- Description
The CADD phred score >= 10
Retrieve SNV summary of a gene
This endpoint allows you to retrieve the summary of SNV variants of a gene.
Path parameters
- Name
geneName- Type
- string
- Description
The name of the gene
Request
curl -G https://api.genohub.org/v1/genes/APOE/snv/summary
Response
{
"total": 1470,
"common": 16,
"lowfreq": 74,
"rare": 1380,
"singletons": 634,
"doubletons": 274,
"exonic": 340,
"utr": 151,
"ncrna": 0,
"intronic": 562,
"downstream": 0,
"intergenic": 32,
"upstream": 385,
"splicing": 0,
"drugresponse": 3,
"pathogenic": 11,
"likelypathogenic": 0,
"benign": 4,
"likelybenign": 13,
"conflicting": 1,
"unknown": 6,
// ...
}
Retrieve INDEL summary of a gene
This endpoint allows you to retrieve the summary of INDEL variants of a gene.
Path parameters
- Name
geneName- Type
- string
- Description
The name of the gene
Request
curl -G https://api.genohub.org/v1/genes/APOE/indel/summary
Response
{
"total": 86,
"common": 0,
"lowfreq": 4,
"rare": 82,
"singletons": 34,
"doubletons": 15,
"exonic": 8,
"utr": 10,
"ncrna": 0,
"intronic": 42,
"downstream": 0,
"intergenic": 2,
"upstream": 24,
"splicing": 0,
"drugresponse": 0,
"pathogenic": 1,
"likelypathogenic": 0,
"benign": 0,
"likelybenign": 1,
"conflicting": 0,
"unknown": 0,
// ...
}
Retrieve SNV summary of a region
This endpoint allows you to retrieve the summary of SNV variants of a region.
Path parameters
- Name
geneName- Type
- string
- Description
The name of the gene
Request
curl -G https://api.genohub.org/v1/regions/19-44851820-44908922/snv/summary
Response
{
"total": 15104,
"common": 334,
"lowfreq": 1231,
"rare": 13539,
"singletons": 6308,
"doubletons": 2421,
"exonic": 1054,
"utr": 912,
"ncrna": 2196,
"intronic": 12408,
"downstream": 329,
"intergenic": 30,
"upstream": 361,
"splicing": 10,
"drugresponse": 3,
"pathogenic": 6,
"likelypathogenic": 0,
"benign": 11,
"likelybenign": 6,
"conflicting": 1,
"unknown": 4,
// ...
}
Retrieve INDEL summary of a region
This endpoint allows you to retrieve the summary of INDEL variants of a region.
Path parameters
- Name
geneName- Type
- string
- Description
The name of the gene
Request
curl -G https://api.genohub.org/v1/regions/19-44851820-44908922/indel/summary
Response
{
"total": 1296,
"common": 124,
"lowfreq": 253,
"rare": 919,
"singletons": 302,
"doubletons": 154,
"exonic": 31,
"utr": 76,
"ncrna": 181,
"intronic": 1134,
"downstream": 29,
"intergenic": 2,
"upstream": 24,
"splicing": 0,
"drugresponse": 0,
"pathogenic": 1,
"likelypathogenic": 0,
"benign": 0,
"likelybenign": 1,
"conflicting": 0,
"unknown": 0,
// ...
}