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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 22-50523901-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=50523901&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 50523901,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000395693.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.511C>T",
"hgvs_p": "p.Arg171Trp",
"transcript": "NM_005138.3",
"protein_id": "NP_005129.2",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 266,
"cds_start": 511,
"cds_end": null,
"cds_length": 801,
"cdna_start": 651,
"cdna_end": null,
"cdna_length": 984,
"mane_select": "ENST00000395693.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.511C>T",
"hgvs_p": "p.Arg171Trp",
"transcript": "ENST00000395693.8",
"protein_id": "ENSP00000379046.4",
"transcript_support_level": 1,
"aa_start": 171,
"aa_end": null,
"aa_length": 266,
"cds_start": 511,
"cds_end": null,
"cds_length": 801,
"cdna_start": 651,
"cdna_end": null,
"cdna_length": 984,
"mane_select": "NM_005138.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCAPH2",
"gene_hgnc_id": 25071,
"hgvs_c": "c.*526G>A",
"hgvs_p": null,
"transcript": "NM_152299.4",
"protein_id": "NP_689512.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 605,
"cds_start": -4,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3337,
"mane_select": "ENST00000420993.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCAPH2",
"gene_hgnc_id": 25071,
"hgvs_c": "c.*526G>A",
"hgvs_p": null,
"transcript": "ENST00000420993.7",
"protein_id": "ENSP00000410088.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 605,
"cds_start": -4,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3337,
"mane_select": "NM_152299.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.511C>T",
"hgvs_p": "p.Arg171Trp",
"transcript": "NM_001169109.2",
"protein_id": "NP_001162580.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 266,
"cds_start": 511,
"cds_end": null,
"cds_length": 801,
"cdna_start": 721,
"cdna_end": null,
"cdna_length": 1054,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.511C>T",
"hgvs_p": "p.Arg171Trp",
"transcript": "NM_001169110.1",
"protein_id": "NP_001162581.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 266,
"cds_start": 511,
"cds_end": null,
"cds_length": 801,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.511C>T",
"hgvs_p": "p.Arg171Trp",
"transcript": "NM_001169111.2",
"protein_id": "NP_001162582.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 266,
"cds_start": 511,
"cds_end": null,
"cds_length": 801,
"cdna_start": 681,
"cdna_end": null,
"cdna_length": 1014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.511C>T",
"hgvs_p": "p.Arg171Trp",
"transcript": "ENST00000252785.3",
"protein_id": "ENSP00000252785.3",
"transcript_support_level": 2,
"aa_start": 171,
"aa_end": null,
"aa_length": 266,
"cds_start": 511,
"cds_end": null,
"cds_length": 801,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 992,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.511C>T",
"hgvs_p": "p.Arg171Trp",
"transcript": "ENST00000535425.5",
"protein_id": "ENSP00000444242.1",
"transcript_support_level": 2,
"aa_start": 171,
"aa_end": null,
"aa_length": 266,
"cds_start": 511,
"cds_end": null,
"cds_length": 801,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.511C>T",
"hgvs_p": "p.Arg171Trp",
"transcript": "ENST00000543927.6",
"protein_id": "ENSP00000444433.1",
"transcript_support_level": 2,
"aa_start": 171,
"aa_end": null,
"aa_length": 266,
"cds_start": 511,
"cds_end": null,
"cds_length": 801,
"cdna_start": 740,
"cdna_end": null,
"cdna_length": 1068,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCAPH2",
"gene_hgnc_id": 25071,
"hgvs_c": "c.*526G>A",
"hgvs_p": null,
"transcript": "NM_001185011.2",
"protein_id": "NP_001171940.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 606,
"cds_start": -4,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3340,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCAPH2",
"gene_hgnc_id": 25071,
"hgvs_c": "c.*526G>A",
"hgvs_p": null,
"transcript": "XM_005261912.5",
"protein_id": "XP_005261969.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 579,
"cds_start": -4,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3395,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCAPH2",
"gene_hgnc_id": 25071,
"hgvs_c": "c.*526G>A",
"hgvs_p": null,
"transcript": "XM_017028793.3",
"protein_id": "XP_016884282.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCAPH2",
"gene_hgnc_id": 25071,
"hgvs_c": "c.*526G>A",
"hgvs_p": null,
"transcript": "XM_011530685.3",
"protein_id": "XP_011528987.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 426,
"cds_start": -4,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCAPH2",
"gene_hgnc_id": 25071,
"hgvs_c": "c.*526G>A",
"hgvs_p": null,
"transcript": "XM_047441352.1",
"protein_id": "XP_047297308.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 425,
"cds_start": -4,
"cds_end": null,
"cds_length": 1278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2808,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCAPH2",
"gene_hgnc_id": 25071,
"hgvs_c": "c.*526G>A",
"hgvs_p": null,
"transcript": "XM_047441353.1",
"protein_id": "XP_047297309.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 311,
"cds_start": -4,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCAPH2",
"gene_hgnc_id": 25071,
"hgvs_c": "c.*526G>A",
"hgvs_p": null,
"transcript": "XM_047441354.1",
"protein_id": "XP_047297310.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 310,
"cds_start": -4,
"cds_end": null,
"cds_length": 933,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272821",
"gene_hgnc_id": null,
"hgvs_c": "n.-25G>A",
"hgvs_p": null,
"transcript": "ENST00000608319.1",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.*5C>T",
"hgvs_p": null,
"transcript": "ENST00000638598.2",
"protein_id": "ENSP00000491753.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 167,
"cds_start": -4,
"cds_end": null,
"cds_length": 506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"dbsnp": "rs28937598",
"frequency_reference_population": 0.0000061971614,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000615825,
"gnomad_genomes_af": 0.00000657082,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9905736446380615,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.838,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6162,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.47,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": -0.045,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM5,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM5",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000395693.8",
"gene_symbol": "SCO2",
"hgnc_id": 10604,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.511C>T",
"hgvs_p": "p.Arg171Trp"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000420993.7",
"gene_symbol": "NCAPH2",
"hgnc_id": 25071,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*526G>A",
"hgvs_p": null
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000608319.1",
"gene_symbol": "ENSG00000272821",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-25G>A",
"hgvs_p": null
}
],
"clinvar_disease": " due to cytochrome c oxidase deficiency 1, fatal infantile,Cardioencephalomyopathy,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}