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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: 2-168968498-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=168968498&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 168968498,
"ref": "A",
"alt": "G",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000650372.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2012-8T>C",
"hgvs_p": null,
"transcript": "NM_003742.4",
"protein_id": "NP_003733.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1321,
"cds_start": -4,
"cds_end": null,
"cds_length": 3966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6934,
"mane_select": "ENST00000650372.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2012-8T>C",
"hgvs_p": null,
"transcript": "ENST00000650372.1",
"protein_id": "ENSP00000497931.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1321,
"cds_start": -4,
"cds_end": null,
"cds_length": 3966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6934,
"mane_select": "NM_003742.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.329-8T>C",
"hgvs_p": null,
"transcript": "ENST00000649448.1",
"protein_id": "ENSP00000497165.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 780,
"cds_start": -4,
"cds_end": null,
"cds_length": 2343,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "n.*482-8T>C",
"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": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2114-8T>C",
"hgvs_p": null,
"transcript": "XM_011512078.3",
"protein_id": "XP_011510380.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1355,
"cds_start": -4,
"cds_end": null,
"cds_length": 4068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4974,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2054-8T>C",
"hgvs_p": null,
"transcript": "XM_006712817.4",
"protein_id": "XP_006712880.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1335,
"cds_start": -4,
"cds_end": null,
"cds_length": 4008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2114-8T>C",
"hgvs_p": null,
"transcript": "XM_017005165.2",
"protein_id": "XP_016860654.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1314,
"cds_start": -4,
"cds_end": null,
"cds_length": 3945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4287,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1343-8T>C",
"hgvs_p": null,
"transcript": "XM_017005166.2",
"protein_id": "XP_016860655.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1098,
"cds_start": -4,
"cds_end": null,
"cds_length": 3297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2114-8T>C",
"hgvs_p": null,
"transcript": "XM_011512080.3",
"protein_id": "XP_011510382.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 936,
"cds_start": -4,
"cds_end": null,
"cds_length": 2811,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.797-8T>C",
"hgvs_p": null,
"transcript": "XM_017005167.2",
"protein_id": "XP_016860656.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 916,
"cds_start": -4,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"dbsnp": "rs769910565",
"frequency_reference_population": 0.0000013737169,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000137372,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7799999713897705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.006534866522997618,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_ADA",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.19,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.24,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.0065348664094932,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000650372.1",
"gene_symbol": "ABCB11",
"hgnc_id": 42,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2012-8T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Progressive familial intrahepatic cholestasis type 2,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided|Progressive familial intrahepatic cholestasis type 2",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}