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


GET/v1/genes/:geneName/snv/summary

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

GET
/v1/genes/:geneName/snv/summary
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,
    // ...
}

GET/v1/genes/:geneName/indel/summary

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

GET
/v1/genes/:geneName/indel/summary
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,
    // ...
}

GET/v1/regions/:region/snv/summary

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

GET
/v1/regions/:region/snv/summary
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,
    // ...
}

GET/v1/regions/:region/indel/summary

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

GET
/v1/regions/:region/indel/summary
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,
    //  ...
}