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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: 17-50190816-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50190816&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 50190816,
"ref": "C",
"alt": "T",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_000088.4",
"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": 51,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.2343+1G>A",
"hgvs_p": null,
"transcript": "NM_000088.4",
"protein_id": "NP_000079.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1464,
"cds_start": -4,
"cds_end": null,
"cds_length": 4395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5914,
"mane_select": "ENST00000225964.10",
"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": 51,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.2343+1G>A",
"hgvs_p": null,
"transcript": "ENST00000225964.10",
"protein_id": "ENSP00000225964.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1464,
"cds_start": -4,
"cds_end": null,
"cds_length": 4395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5914,
"mane_select": "NM_000088.4",
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "n.108+1G>A",
"hgvs_p": null,
"transcript": "ENST00000494334.1",
"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": 396,
"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": 48,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.2145+1G>A",
"hgvs_p": null,
"transcript": "XM_011524341.2",
"protein_id": "XP_011522643.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1398,
"cds_start": -4,
"cds_end": null,
"cds_length": 4197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5716,
"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": 49,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.2343+1G>A",
"hgvs_p": null,
"transcript": "XM_005257058.5",
"protein_id": "XP_005257115.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1374,
"cds_start": -4,
"cds_end": null,
"cds_length": 4125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5644,
"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": 38,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.1425+1G>A",
"hgvs_p": null,
"transcript": "XM_005257059.5",
"protein_id": "XP_005257116.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": -4,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "n.*93G>A",
"hgvs_p": null,
"transcript": "ENST00000476387.1",
"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": 600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"dbsnp": "rs1114167378",
"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": 0.3499999940395355,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9279999732971191,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.809,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 1,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999988247793601,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Moderate,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000088.4",
"gene_symbol": "COL1A1",
"hgnc_id": 2197,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2343+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": "8 conditions,Osteogenesis imperfecta type I",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Osteogenesis imperfecta type I|8 conditions",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}