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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: 16-173471-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=173471&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"gene_symbol": "HBA2",
"hgnc_id": 4824,
"hgvs_c": "c.301-1G>A",
"hgvs_p": null,
"inheritance_mode": "AR,AD",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000517.6",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000294455",
"hgnc_id": null,
"hgvs_c": "n.252C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 14,
"score": 14,
"transcript": "ENST00000723703.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.18,
"chr": "16",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": " 7, familial, nondeletional,Erythrocytosis,HEMOGLOBIN CLINICO-MADRID,Heinz body anemia,Hemoglobin H disease,alpha Thalassemia",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.18000000715255737,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 142,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 576,
"cdna_start": null,
"cds_end": null,
"cds_length": 429,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_000517.6",
"gene_hgnc_id": 4824,
"gene_symbol": "HBA2",
"hgvs_c": "c.301-1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000251595.11",
"protein_coding": true,
"protein_id": "NP_000508.1",
"strand": true,
"transcript": "NM_000517.6",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 142,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 576,
"cdna_start": null,
"cds_end": null,
"cds_length": 429,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000251595.11",
"gene_hgnc_id": 4824,
"gene_symbol": "HBA2",
"hgvs_c": "c.301-1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000517.6",
"protein_coding": true,
"protein_id": "ENSP00000251595.6",
"strand": true,
"transcript": "ENST00000251595.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 640,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000482565.1",
"gene_hgnc_id": 4824,
"gene_symbol": "HBA2",
"hgvs_c": "n.437-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000482565.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 114,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 492,
"cdna_start": null,
"cds_end": null,
"cds_length": 345,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000866237.1",
"gene_hgnc_id": 4824,
"gene_symbol": "HBA2",
"hgvs_c": "c.301-85G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536296.1",
"strand": true,
"transcript": "ENST00000866237.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 110,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 513,
"cdna_start": null,
"cds_end": null,
"cds_length": 333,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000397806.1",
"gene_hgnc_id": 4824,
"gene_symbol": "HBA2",
"hgvs_c": "c.205-1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000380908.1",
"strand": true,
"transcript": "ENST00000397806.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 253,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000723703.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000294455",
"hgvs_c": "n.252C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000723703.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 248,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000723699.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000294455",
"hgvs_c": "n.200+40C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000723699.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 283,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000723700.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000294455",
"hgvs_c": "n.204+36C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000723700.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 221,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000723701.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000294455",
"hgvs_c": "n.178+57C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000723701.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 236,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000723702.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000294455",
"hgvs_c": "n.200+40C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000723702.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 132,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 403,
"cdna_start": null,
"cds_end": null,
"cds_length": 401,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000484216.1",
"gene_hgnc_id": 4824,
"gene_symbol": "HBA2",
"hgvs_c": "c.*8G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495899.1",
"strand": true,
"transcript": "ENST00000484216.1",
"transcript_support_level": 1
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999985151043037,
"dbsnp": "rs587776827",
"effect": "splice_acceptor_variant,intron_variant",
"frequency_reference_population": 6.8593783e-7,
"gene_hgnc_id": 4824,
"gene_symbol": "HBA2",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.85938e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely pathogenic",
"phenotype_combined": "HEMOGLOBIN CLINICO-MADRID|Hemoglobin H disease, nondeletional|alpha Thalassemia|alpha Thalassemia;Erythrocytosis, familial, 7;Heinz body anemia;Hemoglobin H disease",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.576,
"pos": 173471,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9259999990463257,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.99,
"transcript": "NM_000517.6"
}
]
}