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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: 5-147831577-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=147831577&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 147831577,
"ref": "T",
"alt": "A",
"effect": "initiator_codon_variant",
"transcript": "ENST00000296695.10",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK1",
"gene_hgnc_id": 11244,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "NM_001379610.1",
"protein_id": "NP_001366539.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 79,
"cds_start": 1,
"cds_end": null,
"cds_length": 240,
"cdna_start": 95,
"cdna_end": null,
"cdna_length": 413,
"mane_select": "ENST00000296695.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK1",
"gene_hgnc_id": 11244,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000296695.10",
"protein_id": "ENSP00000296695.5",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 79,
"cds_start": 1,
"cds_end": null,
"cds_length": 240,
"cdna_start": 95,
"cdna_end": null,
"cdna_length": 413,
"mane_select": "NM_001379610.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK1",
"gene_hgnc_id": 11244,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "NM_001354966.2",
"protein_id": "NP_001341895.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 79,
"cds_start": 1,
"cds_end": null,
"cds_length": 240,
"cdna_start": 288,
"cdna_end": null,
"cdna_length": 606,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK1",
"gene_hgnc_id": 11244,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "NM_003122.5",
"protein_id": "NP_003113.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 79,
"cds_start": 1,
"cds_end": null,
"cds_length": 240,
"cdna_start": 255,
"cdna_end": null,
"cdna_length": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK1",
"gene_hgnc_id": 11244,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000510027.2",
"protein_id": "ENSP00000427376.1",
"transcript_support_level": 3,
"aa_start": 1,
"aa_end": null,
"aa_length": 65,
"cds_start": 1,
"cds_end": null,
"cds_length": 198,
"cdna_start": 59,
"cdna_end": null,
"cdna_length": 1188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK1",
"gene_hgnc_id": 11244,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "XM_047417625.1",
"protein_id": "XP_047273581.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 79,
"cds_start": 1,
"cds_end": null,
"cds_length": 240,
"cdna_start": 332,
"cdna_end": null,
"cdna_length": 650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK1",
"gene_hgnc_id": 11244,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "XM_047417626.1",
"protein_id": "XP_047273582.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 79,
"cds_start": 1,
"cds_end": null,
"cds_length": 240,
"cdna_start": 365,
"cdna_end": null,
"cdna_length": 683,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124901101",
"gene_hgnc_id": null,
"hgvs_c": "n.535T>A",
"hgvs_p": null,
"transcript": "XR_007058987.1",
"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": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPINK1",
"gene_hgnc_id": 11244,
"dbsnp": "rs369163833",
"frequency_reference_population": 0.000006569439,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000656944,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9894239902496338,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.625,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.282,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000296695.10",
"gene_symbol": "SPINK1",
"hgnc_id": 11244,
"effects": [
"initiator_codon_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_007058987.1",
"gene_symbol": "LOC124901101",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.535T>A",
"hgvs_p": null
}
],
"clinvar_disease": "Hereditary pancreatitis,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:3 US:1",
"phenotype_combined": "not provided|Hereditary pancreatitis",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}