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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: 3-33016819-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=33016819&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 33016819,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_000404.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.1369C>T",
"hgvs_p": "p.Arg457*",
"transcript": "NM_000404.4",
"protein_id": "NP_000395.3",
"transcript_support_level": null,
"aa_start": 457,
"aa_end": null,
"aa_length": 677,
"cds_start": 1369,
"cds_end": null,
"cds_length": 2034,
"cdna_start": 1430,
"cdna_end": null,
"cdna_length": 2523,
"mane_select": "ENST00000307363.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.1369C>T",
"hgvs_p": "p.Arg457*",
"transcript": "ENST00000307363.10",
"protein_id": "ENSP00000306920.4",
"transcript_support_level": 1,
"aa_start": 457,
"aa_end": null,
"aa_length": 677,
"cds_start": 1369,
"cds_end": null,
"cds_length": 2034,
"cdna_start": 1430,
"cdna_end": null,
"cdna_length": 2523,
"mane_select": "NM_000404.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.976C>T",
"hgvs_p": "p.Arg326*",
"transcript": "ENST00000307377.12",
"protein_id": "ENSP00000305920.8",
"transcript_support_level": 1,
"aa_start": 326,
"aa_end": null,
"aa_length": 546,
"cds_start": 976,
"cds_end": null,
"cds_length": 1641,
"cdna_start": 1037,
"cdna_end": null,
"cdna_length": 2018,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.1513C>T",
"hgvs_p": "p.Arg505*",
"transcript": "NM_001317040.2",
"protein_id": "NP_001303969.2",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 725,
"cds_start": 1513,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1574,
"cdna_end": null,
"cdna_length": 2667,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.1279C>T",
"hgvs_p": "p.Arg427*",
"transcript": "NM_001079811.3",
"protein_id": "NP_001073279.2",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 647,
"cds_start": 1279,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 1398,
"cdna_end": null,
"cdna_length": 2491,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.1279C>T",
"hgvs_p": "p.Arg427*",
"transcript": "ENST00000399402.7",
"protein_id": "ENSP00000382333.2",
"transcript_support_level": 2,
"aa_start": 427,
"aa_end": null,
"aa_length": 647,
"cds_start": 1279,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 1411,
"cdna_end": null,
"cdna_length": 2512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.1369C>T",
"hgvs_p": "p.Arg457*",
"transcript": "NM_001393580.1",
"protein_id": "NP_001380509.1",
"transcript_support_level": null,
"aa_start": 457,
"aa_end": null,
"aa_length": 588,
"cds_start": 1369,
"cds_end": null,
"cds_length": 1767,
"cdna_start": 1430,
"cdna_end": null,
"cdna_length": 2309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.976C>T",
"hgvs_p": "p.Arg326*",
"transcript": "NM_001135602.3",
"protein_id": "NP_001129074.2",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 546,
"cds_start": 976,
"cds_end": null,
"cds_length": 1641,
"cdna_start": 1037,
"cdna_end": null,
"cdna_length": 2130,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.468C>T",
"hgvs_p": null,
"transcript": "ENST00000461475.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 816,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.406C>T",
"hgvs_p": null,
"transcript": "ENST00000467571.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 517,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.621C>T",
"hgvs_p": null,
"transcript": "ENST00000497796.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"dbsnp": "rs72555359",
"frequency_reference_population": 0.000008054972,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000820926,
"gnomad_genomes_af": 0.00000657263,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6299999952316284,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.63,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.971,
"phylop100way_prediction": "Uncertain_significance",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000404.4",
"gene_symbol": "GLB1",
"hgnc_id": 4298,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1369C>T",
"hgvs_p": "p.Arg457*"
}
],
"clinvar_disease": " MPS-IV-B,GM1 gangliosidosis,GM1 gangliosidosis type 2,GM1 gangliosidosis type 3,Infantile GM1 gangliosidosis,Mucopolysaccharidosis,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8",
"phenotype_combined": "Infantile GM1 gangliosidosis|Mucopolysaccharidosis, MPS-IV-B;GM1 gangliosidosis type 3;Infantile GM1 gangliosidosis;GM1 gangliosidosis type 2|GM1 gangliosidosis;Mucopolysaccharidosis, MPS-IV-B|GM1 gangliosidosis|not provided|GM1 gangliosidosis type 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}