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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: 5-150056218-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=150056218&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 150056218,
"ref": "C",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "ENST00000675795.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2442+1G>T",
"hgvs_p": null,
"transcript": "NM_001288705.3",
"protein_id": "NP_001275634.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 972,
"cds_start": -4,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3820,
"mane_select": "ENST00000675795.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2442+1G>T",
"hgvs_p": null,
"transcript": "ENST00000675795.1",
"protein_id": "ENSP00000501699.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 972,
"cds_start": -4,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3820,
"mane_select": "NM_001288705.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2442+1G>T",
"hgvs_p": null,
"transcript": "ENST00000286301.7",
"protein_id": "ENSP00000286301.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 972,
"cds_start": -4,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3989,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "n.*263+1G>T",
"hgvs_p": null,
"transcript": "ENST00000504875.5",
"protein_id": "ENSP00000422212.1",
"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": 3697,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2442+1G>T",
"hgvs_p": null,
"transcript": "NM_001349736.2",
"protein_id": "NP_001336665.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 972,
"cds_start": -4,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4064,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2442+1G>T",
"hgvs_p": null,
"transcript": "NM_001375320.1",
"protein_id": "NP_001362249.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 972,
"cds_start": -4,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4083,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.2442+1G>T",
"hgvs_p": null,
"transcript": "NM_005211.4",
"protein_id": "NP_005202.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 972,
"cds_start": -4,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3978,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "c.1998+1G>T",
"hgvs_p": null,
"transcript": "NM_001375321.1",
"protein_id": "NP_001362250.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 824,
"cds_start": -4,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3749,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "n.*416+1G>T",
"hgvs_p": null,
"transcript": "ENST00000515068.1",
"protein_id": "ENSP00000427545.1",
"transcript_support_level": 5,
"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": 723,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "n.2406+1G>T",
"hgvs_p": null,
"transcript": "NR_109969.2",
"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": 3657,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"hgvs_c": "n.2335+1G>T",
"hgvs_p": null,
"transcript": "NR_164679.1",
"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": 3586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CSF1R",
"gene_hgnc_id": 2433,
"dbsnp": "rs587777246",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09000000357627869,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9259999990463257,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.887,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.99,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999946188727699,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000675795.1",
"gene_symbol": "CSF1R",
"hgnc_id": 2433,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2442+1G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Hereditary diffuse leukoencephalopathy with spheroids",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Hereditary diffuse leukoencephalopathy with spheroids",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}