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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: 2-168964259-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=168964259&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 168964259,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000650372.1",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2125G>A",
"hgvs_p": "p.Glu709Lys",
"transcript": "NM_003742.4",
"protein_id": "NP_003733.2",
"transcript_support_level": null,
"aa_start": 709,
"aa_end": null,
"aa_length": 1321,
"cds_start": 2125,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 2252,
"cdna_end": null,
"cdna_length": 6934,
"mane_select": "ENST00000650372.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2125G>A",
"hgvs_p": "p.Glu709Lys",
"transcript": "ENST00000650372.1",
"protein_id": "ENSP00000497931.1",
"transcript_support_level": null,
"aa_start": 709,
"aa_end": null,
"aa_length": 1321,
"cds_start": 2125,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 2252,
"cdna_end": null,
"cdna_length": 6934,
"mane_select": "NM_003742.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.442G>A",
"hgvs_p": "p.Glu148Lys",
"transcript": "ENST00000649448.1",
"protein_id": "ENSP00000497165.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 780,
"cds_start": 442,
"cds_end": null,
"cds_length": 2343,
"cdna_start": 442,
"cdna_end": null,
"cdna_length": 2983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2227G>A",
"hgvs_p": "p.Glu743Lys",
"transcript": "XM_011512078.3",
"protein_id": "XP_011510380.1",
"transcript_support_level": null,
"aa_start": 743,
"aa_end": null,
"aa_length": 1355,
"cds_start": 2227,
"cds_end": null,
"cds_length": 4068,
"cdna_start": 2354,
"cdna_end": null,
"cdna_length": 4974,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2167G>A",
"hgvs_p": "p.Glu723Lys",
"transcript": "XM_006712817.4",
"protein_id": "XP_006712880.1",
"transcript_support_level": null,
"aa_start": 723,
"aa_end": null,
"aa_length": 1335,
"cds_start": 2167,
"cds_end": null,
"cds_length": 4008,
"cdna_start": 2294,
"cdna_end": null,
"cdna_length": 4181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2227G>A",
"hgvs_p": "p.Glu743Lys",
"transcript": "XM_017005165.2",
"protein_id": "XP_016860654.1",
"transcript_support_level": null,
"aa_start": 743,
"aa_end": null,
"aa_length": 1314,
"cds_start": 2227,
"cds_end": null,
"cds_length": 3945,
"cdna_start": 2354,
"cdna_end": null,
"cdna_length": 4287,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1456G>A",
"hgvs_p": "p.Glu486Lys",
"transcript": "XM_017005166.2",
"protein_id": "XP_016860655.1",
"transcript_support_level": null,
"aa_start": 486,
"aa_end": null,
"aa_length": 1098,
"cds_start": 1456,
"cds_end": null,
"cds_length": 3297,
"cdna_start": 1549,
"cdna_end": null,
"cdna_length": 3436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2227G>A",
"hgvs_p": "p.Glu743Lys",
"transcript": "XM_011512080.3",
"protein_id": "XP_011510382.1",
"transcript_support_level": null,
"aa_start": 743,
"aa_end": null,
"aa_length": 936,
"cds_start": 2227,
"cds_end": null,
"cds_length": 2811,
"cdna_start": 2354,
"cdna_end": null,
"cdna_length": 3053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.910G>A",
"hgvs_p": "p.Glu304Lys",
"transcript": "XM_017005167.2",
"protein_id": "XP_016860656.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 916,
"cds_start": 910,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 1106,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "n.*595G>A",
"hgvs_p": null,
"transcript": "ENST00000439188.1",
"protein_id": "ENSP00000416058.1",
"transcript_support_level": 2,
"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": 2822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "n.*595G>A",
"hgvs_p": null,
"transcript": "ENST00000439188.1",
"protein_id": "ENSP00000416058.1",
"transcript_support_level": 2,
"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": 2822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"dbsnp": "rs201800225",
"frequency_reference_population": 0.0001254095,
"hom_count_reference_population": 0,
"allele_count_reference_population": 197,
"gnomad_exomes_af": 0.000131767,
"gnomad_genomes_af": 0.0000659265,
"gnomad_exomes_ac": 187,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.014417946338653564,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.235,
"revel_prediction": "Benign",
"alphamissense_score": 0.076,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.918,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000650372.1",
"gene_symbol": "ABCB11",
"hgnc_id": 42,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2125G>A",
"hgvs_p": "p.Glu709Lys"
}
],
"clinvar_disease": "ABCB11-related disorder,Benign recurrent intrahepatic cholestasis type 2,Progressive familial intrahepatic cholestasis type 2,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:6 LB:1",
"phenotype_combined": "not provided|Benign recurrent intrahepatic cholestasis type 2|Progressive familial intrahepatic cholestasis type 2;Benign recurrent intrahepatic cholestasis type 2|ABCB11-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}