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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: 2-42770143-C-CA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=42770143&ref=C&alt=CA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 42770143,
"ref": "C",
"alt": "CA",
"effect": "frameshift_variant,splice_region_variant",
"transcript": "ENST00000294973.11",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAAO",
"gene_hgnc_id": 4796,
"hgvs_c": "c.483dupT",
"hgvs_p": "p.Asp162fs",
"transcript": "NM_012205.3",
"protein_id": "NP_036337.2",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 286,
"cds_start": 483,
"cds_end": null,
"cds_length": 861,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 1256,
"mane_select": "ENST00000294973.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAAO",
"gene_hgnc_id": 4796,
"hgvs_c": "c.483dupT",
"hgvs_p": "p.Asp162fs",
"transcript": "ENST00000294973.11",
"protein_id": "ENSP00000294973.6",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 286,
"cds_start": 483,
"cds_end": null,
"cds_length": 861,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 1256,
"mane_select": "NM_012205.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAAO",
"gene_hgnc_id": 4796,
"hgvs_c": "c.381dupT",
"hgvs_p": "p.Asp128fs",
"transcript": "ENST00000431905.1",
"protein_id": "ENSP00000412601.1",
"transcript_support_level": 3,
"aa_start": 127,
"aa_end": null,
"aa_length": 175,
"cds_start": 381,
"cds_end": null,
"cds_length": 530,
"cdna_start": 678,
"cdna_end": null,
"cdna_length": 827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAAO",
"gene_hgnc_id": 4796,
"hgvs_c": "c.393dupT",
"hgvs_p": "p.Asp132fs",
"transcript": "XM_011532729.4",
"protein_id": "XP_011531031.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 256,
"cds_start": 393,
"cds_end": null,
"cds_length": 771,
"cdna_start": 440,
"cdna_end": null,
"cdna_length": 1166,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAAO",
"gene_hgnc_id": 4796,
"hgvs_c": "c.381dupT",
"hgvs_p": "p.Asp128fs",
"transcript": "XM_011532730.4",
"protein_id": "XP_011531032.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 252,
"cds_start": 381,
"cds_end": null,
"cds_length": 759,
"cdna_start": 689,
"cdna_end": null,
"cdna_length": 1415,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAAO",
"gene_hgnc_id": 4796,
"hgvs_c": "n.827dupT",
"hgvs_p": null,
"transcript": "ENST00000402698.6",
"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": 1522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAAO",
"gene_hgnc_id": 4796,
"hgvs_c": "n.388dupT",
"hgvs_p": null,
"transcript": "ENST00000404451.7",
"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": 651,
"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": "HAAO",
"gene_hgnc_id": 4796,
"hgvs_c": "n.846dupT",
"hgvs_p": null,
"transcript": "ENST00000406924.6",
"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": 1103,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HAAO",
"gene_hgnc_id": 4796,
"dbsnp": "rs527656756",
"frequency_reference_population": 0.000011222589,
"hom_count_reference_population": 0,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000110213,
"gnomad_genomes_af": 0.0000131423,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.065,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"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": "ENST00000294973.11",
"gene_symbol": "HAAO",
"hgnc_id": 4796,
"effects": [
"frameshift_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.483dupT",
"hgvs_p": "p.Asp162fs"
}
],
"clinvar_disease": " and limb defects syndrome 1, cardiac, renal,Congenital NAD deficiency disorder,Vertebral",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Congenital NAD deficiency disorder|Vertebral, cardiac, renal, and limb defects syndrome 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}