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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: X-153803925-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153803925&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PDZD4",
"hgnc_id": 21167,
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.His586Tyr",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001303512.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": 0.0817,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.63,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.1405690610408783,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 775,
"aa_ref": "H",
"aa_start": 586,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3761,
"cdna_start": 2002,
"cds_end": null,
"cds_length": 2328,
"cds_start": 1756,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001303512.2",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.His586Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000393758.7",
"protein_coding": true,
"protein_id": "NP_001290441.1",
"strand": false,
"transcript": "NM_001303512.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 775,
"aa_ref": "H",
"aa_start": 586,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3761,
"cdna_start": 2002,
"cds_end": null,
"cds_length": 2328,
"cds_start": 1756,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000393758.7",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.His586Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001303512.2",
"protein_coding": true,
"protein_id": "ENSP00000377355.3",
"strand": false,
"transcript": "ENST00000393758.7",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 769,
"aa_ref": "H",
"aa_start": 580,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3689,
"cdna_start": 1930,
"cds_end": null,
"cds_length": 2310,
"cds_start": 1738,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000164640.8",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1738C>T",
"hgvs_p": "p.His580Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000164640.4",
"strand": false,
"transcript": "ENST00000164640.8",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 660,
"aa_ref": "H",
"aa_start": 471,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3418,
"cdna_start": 1661,
"cds_end": null,
"cds_length": 1983,
"cds_start": 1411,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000544474.5",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1411C>T",
"hgvs_p": "p.His471Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000442033.1",
"strand": false,
"transcript": "ENST00000544474.5",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 774,
"aa_ref": "H",
"aa_start": 585,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4144,
"cdna_start": 2385,
"cds_end": null,
"cds_length": 2325,
"cds_start": 1753,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000933007.1",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1753C>T",
"hgvs_p": "p.His585Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603066.1",
"strand": false,
"transcript": "ENST00000933007.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 769,
"aa_ref": "H",
"aa_start": 580,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3743,
"cdna_start": 1984,
"cds_end": null,
"cds_length": 2310,
"cds_start": 1738,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_032512.5",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1738C>T",
"hgvs_p": "p.His580Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_115901.2",
"strand": false,
"transcript": "NM_032512.5",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 694,
"aa_ref": "H",
"aa_start": 505,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3682,
"cdna_start": 1923,
"cds_end": null,
"cds_length": 2085,
"cds_start": 1513,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001303515.2",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1513C>T",
"hgvs_p": "p.His505Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001290444.1",
"strand": false,
"transcript": "NM_001303515.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 688,
"aa_ref": "H",
"aa_start": 499,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3664,
"cdna_start": 1905,
"cds_end": null,
"cds_length": 2067,
"cds_start": 1495,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001303516.2",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1495C>T",
"hgvs_p": "p.His499Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001290445.1",
"strand": false,
"transcript": "NM_001303516.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 688,
"aa_ref": "H",
"aa_start": 499,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3358,
"cdna_start": 1599,
"cds_end": null,
"cds_length": 2067,
"cds_start": 1495,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000933008.1",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1495C>T",
"hgvs_p": "p.His499Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603067.1",
"strand": false,
"transcript": "ENST00000933008.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 673,
"aa_ref": "H",
"aa_start": 484,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4004,
"cdna_start": 2245,
"cds_end": null,
"cds_length": 2022,
"cds_start": 1450,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001303513.3",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1450C>T",
"hgvs_p": "p.His484Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001290442.1",
"strand": false,
"transcript": "NM_001303513.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 660,
"aa_ref": "H",
"aa_start": 471,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3416,
"cdna_start": 1657,
"cds_end": null,
"cds_length": 1983,
"cds_start": 1411,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001303514.2",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1411C>T",
"hgvs_p": "p.His471Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001290443.1",
"strand": false,
"transcript": "NM_001303514.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 627,
"aa_ref": "H",
"aa_start": 438,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3144,
"cdna_start": 1385,
"cds_end": null,
"cds_length": 1884,
"cds_start": 1312,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000933009.1",
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"hgvs_c": "c.1312C>T",
"hgvs_p": "p.His438Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603068.1",
"strand": false,
"transcript": "ENST00000933009.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs782552006",
"effect": "missense_variant",
"frequency_reference_population": 0.0000056588665,
"gene_hgnc_id": 21167,
"gene_symbol": "PDZD4",
"gnomad_exomes_ac": 6,
"gnomad_exomes_af": 0.00000565887,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 3,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.835,
"pos": 153803925,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.173,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001303512.2"
}
]
}