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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: 1-179917952-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=179917952&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 179917952,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000606911.7",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.1465A>G",
"hgvs_p": "p.Thr489Ala",
"transcript": "NM_015602.4",
"protein_id": "NP_056417.2",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 583,
"cds_start": 1465,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 1683,
"cdna_end": null,
"cdna_length": 3807,
"mane_select": "ENST00000606911.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.1465A>G",
"hgvs_p": "p.Thr489Ala",
"transcript": "ENST00000606911.7",
"protein_id": "ENSP00000476687.1",
"transcript_support_level": 1,
"aa_start": 489,
"aa_end": null,
"aa_length": 583,
"cds_start": 1465,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 1683,
"cdna_end": null,
"cdna_length": 3807,
"mane_select": "NM_015602.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.1102A>G",
"hgvs_p": "p.Thr368Ala",
"transcript": "ENST00000435319.8",
"protein_id": "ENSP00000393292.3",
"transcript_support_level": 1,
"aa_start": 368,
"aa_end": null,
"aa_length": 462,
"cds_start": 1102,
"cds_end": null,
"cds_length": 1389,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 3397,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.1513A>G",
"hgvs_p": "p.Thr505Ala",
"transcript": "ENST00000271583.7",
"protein_id": "ENSP00000271583.3",
"transcript_support_level": 5,
"aa_start": 505,
"aa_end": null,
"aa_length": 599,
"cds_start": 1513,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1719,
"cdna_end": null,
"cdna_length": 3044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.1468A>G",
"hgvs_p": "p.Thr490Ala",
"transcript": "NM_001267578.2",
"protein_id": "NP_001254507.1",
"transcript_support_level": null,
"aa_start": 490,
"aa_end": null,
"aa_length": 584,
"cds_start": 1468,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 1686,
"cdna_end": null,
"cdna_length": 3810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.1468A>G",
"hgvs_p": "p.Thr490Ala",
"transcript": "ENST00000528443.6",
"protein_id": "ENSP00000435365.2",
"transcript_support_level": 2,
"aa_start": 490,
"aa_end": null,
"aa_length": 584,
"cds_start": 1468,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 1929,
"cdna_end": null,
"cdna_length": 3685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.667A>G",
"hgvs_p": "p.Thr223Ala",
"transcript": "ENST00000447964.1",
"protein_id": "ENSP00000393613.1",
"transcript_support_level": 3,
"aa_start": 223,
"aa_end": null,
"aa_length": 294,
"cds_start": 667,
"cds_end": null,
"cds_length": 886,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 888,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "n.*227A>G",
"hgvs_p": null,
"transcript": "ENST00000474875.5",
"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": 830,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"dbsnp": "rs375127929",
"frequency_reference_population": 0.00000309764,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000273618,
"gnomad_genomes_af": 0.00000656858,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.35871943831443787,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.342,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1074,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.68,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000606911.7",
"gene_symbol": "TOR1AIP1",
"hgnc_id": 29456,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1465A>G",
"hgvs_p": "p.Thr489Ala"
}
],
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2Y",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2Y",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}