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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: 19-32963536-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=32963536&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "CEP89",
"hgnc_id": 25907,
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_032816.5",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "RPL31P60",
"hgnc_id": 36123,
"hgvs_c": "n.38C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000478450.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 20940,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.87,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8700000047683716,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 783,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5673,
"cdna_start": null,
"cds_end": null,
"cds_length": 2352,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_032816.5",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000305768.10",
"protein_coding": true,
"protein_id": "NP_116205.3",
"strand": false,
"transcript": "NM_032816.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 783,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5673,
"cdna_start": null,
"cds_end": null,
"cds_length": 2352,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000305768.10",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032816.5",
"protein_coding": true,
"protein_id": "ENSP00000306105.4",
"strand": false,
"transcript": "ENST00000305768.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 356,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1340,
"cdna_start": null,
"cds_end": null,
"cds_length": 1071,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000590597.6",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466442.1",
"strand": false,
"transcript": "ENST00000590597.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 216,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 682,
"cdna_start": null,
"cds_end": null,
"cds_length": 651,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000593276.2",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.59+2824G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000467839.1",
"strand": false,
"transcript": "ENST00000593276.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2482,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000586984.6",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "n.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000465141.1",
"strand": false,
"transcript": "ENST00000586984.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 817,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2684,
"cdna_start": null,
"cds_end": null,
"cds_length": 2454,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000959605.1",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629664.1",
"strand": false,
"transcript": "ENST00000959605.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 806,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2692,
"cdna_start": null,
"cds_end": null,
"cds_length": 2421,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000959603.1",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629662.1",
"strand": false,
"transcript": "ENST00000959603.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 789,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2639,
"cdna_start": null,
"cds_end": null,
"cds_length": 2370,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000959604.1",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629663.1",
"strand": false,
"transcript": "ENST00000959604.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 759,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2559,
"cdna_start": null,
"cds_end": null,
"cds_length": 2280,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000909768.1",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579827.1",
"strand": false,
"transcript": "ENST00000909768.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 753,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2511,
"cdna_start": null,
"cds_end": null,
"cds_length": 2262,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000909769.1",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579828.1",
"strand": false,
"transcript": "ENST00000909769.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 727,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5499,
"cdna_start": null,
"cds_end": null,
"cds_length": 2184,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000959602.1",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629661.1",
"strand": false,
"transcript": "ENST00000959602.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 759,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5601,
"cdna_start": null,
"cds_end": null,
"cds_length": 2280,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005259344.4",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005259401.1",
"strand": false,
"transcript": "XM_005259344.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 637,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2346,
"cdna_start": null,
"cds_end": null,
"cds_length": 1914,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017027398.2",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882887.1",
"strand": false,
"transcript": "XM_017027398.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 475,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1681,
"cdna_start": null,
"cds_end": null,
"cds_length": 1428,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047439563.1",
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"hgvs_c": "c.146+2824G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295519.1",
"strand": false,
"transcript": "XM_047439563.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "processed_pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 367,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000478450.1",
"gene_hgnc_id": 36123,
"gene_symbol": "RPL31P60",
"hgvs_c": "n.38C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000478450.1",
"transcript_support_level": 6
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": null,
"canonical": null,
"cdna_end": null,
"cdna_length": null,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intragenic_variant"
],
"exon_count": null,
"exon_rank": null,
"exon_rank_end": null,
"feature": null,
"gene_hgnc_id": 36123,
"gene_symbol": "RPL31P60",
"hgvs_c": "n.32963536C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": null,
"protein_id": null,
"strand": true,
"transcript": null,
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs16967665",
"effect": "intron_variant",
"frequency_reference_population": 0.13764182,
"gene_hgnc_id": 25907,
"gene_symbol": "CEP89",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.166667,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 20937,
"gnomad_genomes_af": 0.137638,
"gnomad_genomes_homalt": 1469,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1470,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.873,
"pos": 32963536,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_032816.5"
}
]
}