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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: 5-32073460-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=32073460&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 32073460,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000438447.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "c.2726-372A>G",
"hgvs_p": null,
"transcript": "NM_178140.4",
"protein_id": "NP_835260.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2839,
"cds_start": -4,
"cds_end": null,
"cds_length": 8520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11984,
"mane_select": "ENST00000438447.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "c.2726-372A>G",
"hgvs_p": null,
"transcript": "ENST00000438447.2",
"protein_id": "ENSP00000402033.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2839,
"cds_start": -4,
"cds_end": null,
"cds_length": 8520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11984,
"mane_select": "NM_178140.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "n.2482-372A>G",
"hgvs_p": null,
"transcript": "ENST00000502489.5",
"protein_id": null,
"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": 3787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "c.2726-372A>G",
"hgvs_p": null,
"transcript": "XM_005248269.5",
"protein_id": "XP_005248326.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2873,
"cds_start": -4,
"cds_end": null,
"cds_length": 8622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12086,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "c.2726-372A>G",
"hgvs_p": null,
"transcript": "XM_011513992.3",
"protein_id": "XP_011512294.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2873,
"cds_start": -4,
"cds_end": null,
"cds_length": 8622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "c.2726-372A>G",
"hgvs_p": null,
"transcript": "XM_011513993.3",
"protein_id": "XP_011512295.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2873,
"cds_start": -4,
"cds_end": null,
"cds_length": 8622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11832,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "c.2726-372A>G",
"hgvs_p": null,
"transcript": "XM_011513994.3",
"protein_id": "XP_011512296.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2861,
"cds_start": -4,
"cds_end": null,
"cds_length": 8586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "c.2450-372A>G",
"hgvs_p": null,
"transcript": "XM_011513996.3",
"protein_id": "XP_011512298.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2781,
"cds_start": -4,
"cds_end": null,
"cds_length": 8346,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "c.1733-372A>G",
"hgvs_p": null,
"transcript": "XM_006714460.3",
"protein_id": "XP_006714523.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2542,
"cds_start": -4,
"cds_end": null,
"cds_length": 7629,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"hgvs_c": "c.1733-372A>G",
"hgvs_p": null,
"transcript": "XM_047416965.1",
"protein_id": "XP_047272921.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2530,
"cds_start": -4,
"cds_end": null,
"cds_length": 7593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDZD2",
"gene_hgnc_id": 18486,
"dbsnp": "rs32793",
"frequency_reference_population": 0.34483394,
"hom_count_reference_population": 10245,
"allele_count_reference_population": 52412,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.344834,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 52412,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 10245,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9399999976158142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.94,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.483,
"phylop100way_prediction": "Benign",
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000438447.2",
"gene_symbol": "PDZD2",
"hgnc_id": 18486,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2726-372A>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}