Summary
On this page, we'll dive into the Summary endpoint you can use to fetch summary statistics for genes and regions programmatically.
Retrieve SNV summary of a gene
This endpoint allows you to retrieve the summary of SNV variants of a gene. Refer to the list at the bottom of of this page to see which properties are included with summary objects.
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. Refer to the list at the bottom of of this page to see which properties are included with summary objects.
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. Refer to the list at the bottom of of this page to see which properties are included with summary objects.
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. Refer to the list at the bottom of of this page to see which properties are included with summary objects.
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,
// ...
}
The summary model
The summary model contains all the statistics information about a gene or a region. Refer to the list at the bottom of of this page to see which properties are included with summary objects.
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