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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: 5-69189765-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=69189765&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 69189765,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_022909.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CENPH",
"gene_hgnc_id": 17268,
"hgvs_c": "c.131T>C",
"hgvs_p": "p.Leu44Pro",
"transcript": "NM_022909.4",
"protein_id": "NP_075060.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 247,
"cds_start": 131,
"cds_end": null,
"cds_length": 744,
"cdna_start": 183,
"cdna_end": null,
"cdna_length": 1354,
"mane_select": "ENST00000283006.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CENPH",
"gene_hgnc_id": 17268,
"hgvs_c": "c.131T>C",
"hgvs_p": "p.Leu44Pro",
"transcript": "ENST00000283006.7",
"protein_id": "ENSP00000283006.2",
"transcript_support_level": 1,
"aa_start": 44,
"aa_end": null,
"aa_length": 247,
"cds_start": 131,
"cds_end": null,
"cds_length": 744,
"cdna_start": 183,
"cdna_end": null,
"cdna_length": 1354,
"mane_select": "NM_022909.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CENPH",
"gene_hgnc_id": 17268,
"hgvs_c": "c.131T>C",
"hgvs_p": "p.Leu44Pro",
"transcript": "ENST00000515001.5",
"protein_id": "ENSP00000426014.1",
"transcript_support_level": 2,
"aa_start": 44,
"aa_end": null,
"aa_length": 228,
"cds_start": 131,
"cds_end": null,
"cds_length": 687,
"cdna_start": 192,
"cdna_end": null,
"cdna_length": 1305,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CENPH",
"gene_hgnc_id": 17268,
"hgvs_c": "c.23T>C",
"hgvs_p": "p.Leu8Pro",
"transcript": "ENST00000502689.1",
"protein_id": "ENSP00000423936.1",
"transcript_support_level": 5,
"aa_start": 8,
"aa_end": null,
"aa_length": 186,
"cds_start": 23,
"cds_end": null,
"cds_length": 561,
"cdna_start": 24,
"cdna_end": null,
"cdna_length": 692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CENPH",
"gene_hgnc_id": 17268,
"hgvs_c": "n.174T>C",
"hgvs_p": null,
"transcript": "ENST00000513575.5",
"protein_id": null,
"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": 437,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CENPH",
"gene_hgnc_id": 17268,
"hgvs_c": "n.120T>C",
"hgvs_p": null,
"transcript": "ENST00000514753.1",
"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": 750,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000295746",
"gene_hgnc_id": null,
"hgvs_c": "n.45A>G",
"hgvs_p": null,
"transcript": "ENST00000732376.1",
"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": 1390,
"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": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000295746",
"gene_hgnc_id": null,
"hgvs_c": "n.25A>G",
"hgvs_p": null,
"transcript": "ENST00000732378.1",
"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": 2497,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CENPH",
"gene_hgnc_id": 17268,
"dbsnp": "rs1025224684",
"frequency_reference_population": 0.0000053474937,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000223265,
"gnomad_genomes_af": 0.0000328226,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8581686615943909,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.426,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.6281,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.991,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_022909.4",
"gene_symbol": "CENPH",
"hgnc_id": 17268,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.131T>C",
"hgvs_p": "p.Leu44Pro"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000732376.1",
"gene_symbol": "ENSG00000295746",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.45A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}