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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: 19-19599328-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=19599328&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 19599328,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_025245.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Leu53Leu",
"transcript": "NM_025245.3",
"protein_id": "NP_079521.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 374,
"cds_start": 157,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 215,
"cdna_end": null,
"cdna_length": 1495,
"mane_select": "ENST00000251203.14",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Leu53Leu",
"transcript": "ENST00000251203.14",
"protein_id": "ENSP00000251203.5",
"transcript_support_level": 1,
"aa_start": 53,
"aa_end": null,
"aa_length": 374,
"cds_start": 157,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 215,
"cdna_end": null,
"cdna_length": 1495,
"mane_select": "NM_025245.3",
"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": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "n.157C>T",
"hgvs_p": null,
"transcript": "ENST00000557978.6",
"protein_id": "ENSP00000453348.1",
"transcript_support_level": 1,
"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": 1416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.-140C>T",
"hgvs_p": null,
"transcript": "XM_011528322.2",
"protein_id": "XP_011526624.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": -4,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Leu53Leu",
"transcript": "XM_011528320.4",
"protein_id": "XP_011526622.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 391,
"cds_start": 157,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 215,
"cdna_end": null,
"cdna_length": 1546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Leu53Leu",
"transcript": "XM_047439472.1",
"protein_id": "XP_047295428.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 246,
"cds_start": 157,
"cds_end": null,
"cds_length": 741,
"cdna_start": 215,
"cdna_end": null,
"cdna_length": 887,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "n.157C>T",
"hgvs_p": null,
"transcript": "ENST00000558222.1",
"protein_id": "ENSP00000453069.1",
"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": 1034,
"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": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "n.215C>T",
"hgvs_p": null,
"transcript": "NR_038198.2",
"protein_id": null,
"transcript_support_level": null,
"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": 1394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.-140C>T",
"hgvs_p": null,
"transcript": "XM_011528322.2",
"protein_id": "XP_011526624.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": -4,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.-104+19183C>T",
"hgvs_p": null,
"transcript": "XM_006722911.4",
"protein_id": "XP_006722974.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": -4,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.-66+19183C>T",
"hgvs_p": null,
"transcript": "XM_047439471.1",
"protein_id": "XP_047295427.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": -4,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1421,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"dbsnp": "rs756115893",
"frequency_reference_population": 0.0000018594411,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000136871,
"gnomad_genomes_af": 0.0000065722,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6100000143051147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.835,
"phylop100way_prediction": "Uncertain_significance",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_025245.3",
"gene_symbol": "PBX4",
"hgnc_id": 13403,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Leu53Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}