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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: 3-180616335-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=180616335&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 180616335,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000476379.6",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.2615C>T",
"hgvs_p": "p.Thr872Ile",
"transcript": "NM_181426.2",
"protein_id": "NP_852091.1",
"transcript_support_level": null,
"aa_start": 872,
"aa_end": null,
"aa_length": 941,
"cds_start": 2615,
"cds_end": null,
"cds_length": 2826,
"cdna_start": 2724,
"cdna_end": null,
"cdna_length": 3848,
"mane_select": "ENST00000476379.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.2615C>T",
"hgvs_p": "p.Thr872Ile",
"transcript": "ENST00000476379.6",
"protein_id": "ENSP00000417960.2",
"transcript_support_level": 2,
"aa_start": 872,
"aa_end": null,
"aa_length": 941,
"cds_start": 2615,
"cds_end": null,
"cds_length": 2826,
"cdna_start": 2724,
"cdna_end": null,
"cdna_length": 3848,
"mane_select": "NM_181426.2",
"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": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "TTC14",
"gene_hgnc_id": 24697,
"hgvs_c": "c.1775-1045G>A",
"hgvs_p": null,
"transcript": "ENST00000382584.8",
"protein_id": "ENSP00000372027.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 653,
"cds_start": -4,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.2423C>T",
"hgvs_p": "p.Thr808Ile",
"transcript": "ENST00000651046.1",
"protein_id": "ENSP00000499175.1",
"transcript_support_level": null,
"aa_start": 808,
"aa_end": null,
"aa_length": 877,
"cds_start": 2423,
"cds_end": null,
"cds_length": 2634,
"cdna_start": 2517,
"cdna_end": null,
"cdna_length": 3582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.164C>T",
"hgvs_p": "p.Thr55Ile",
"transcript": "ENST00000473854.5",
"protein_id": "ENSP00000418482.1",
"transcript_support_level": 2,
"aa_start": 55,
"aa_end": null,
"aa_length": 101,
"cds_start": 164,
"cds_end": null,
"cds_length": 306,
"cdna_start": 166,
"cdna_end": null,
"cdna_length": 487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.131C>T",
"hgvs_p": "p.Thr44Ile",
"transcript": "ENST00000489868.6",
"protein_id": "ENSP00000420025.1",
"transcript_support_level": 3,
"aa_start": 44,
"aa_end": null,
"aa_length": 67,
"cds_start": 131,
"cds_end": null,
"cds_length": 204,
"cdna_start": 131,
"cdna_end": null,
"cdna_length": 526,
"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": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000145075",
"gene_hgnc_id": null,
"hgvs_c": "n.3327C>T",
"hgvs_p": null,
"transcript": "ENST00000651576.1",
"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": 4451,
"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": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1940C>T",
"hgvs_p": null,
"transcript": "ENST00000651922.1",
"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": 2828,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.2691C>T",
"hgvs_p": null,
"transcript": "ENST00000652010.1",
"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": 3799,
"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": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "TTC14",
"gene_hgnc_id": 24697,
"hgvs_c": "c.1775-1045G>A",
"hgvs_p": null,
"transcript": "NM_001288582.2",
"protein_id": "NP_001275511.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 653,
"cds_start": -4,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"dbsnp": "rs202027034",
"frequency_reference_population": 6.844805e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8448e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04449254274368286,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.135,
"revel_prediction": "Benign",
"alphamissense_score": 0.0866,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.771,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.11,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000476379.6",
"gene_symbol": "CCDC39",
"hgnc_id": 25244,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2615C>T",
"hgvs_p": "p.Thr872Ile"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000651576.1",
"gene_symbol": "ENSG00000145075",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3327C>T",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001288582.2",
"gene_symbol": "TTC14",
"hgnc_id": 24697,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1775-1045G>A",
"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
}