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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: 11-5234551-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=5234551&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 5234551,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000643122.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HBD",
"gene_hgnc_id": 4829,
"hgvs_c": "c.-28-90C>T",
"hgvs_p": null,
"transcript": "ENST00000643122.1",
"protein_id": "ENSP00000494708.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 147,
"cds_start": -4,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HBD",
"gene_hgnc_id": 4829,
"hgvs_c": "c.-97-21C>T",
"hgvs_p": null,
"transcript": "ENST00000429817.1",
"protein_id": "ENSP00000393810.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 103,
"cds_start": -4,
"cds_end": null,
"cds_length": 313,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000298932",
"gene_hgnc_id": null,
"hgvs_c": "n.266-8558G>A",
"hgvs_p": null,
"transcript": "ENST00000759072.1",
"protein_id": null,
"transcript_support_level": null,
"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": 336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBD",
"gene_hgnc_id": 4829,
"hgvs_c": "c.-118C>T",
"hgvs_p": null,
"transcript": "NM_000519.4",
"protein_id": "NP_000510.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 147,
"cds_start": -4,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 620,
"mane_select": "ENST00000650601.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBD",
"gene_hgnc_id": 4829,
"hgvs_c": "c.-118C>T",
"hgvs_p": null,
"transcript": "ENST00000650601.1",
"protein_id": "ENSP00000497529.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 147,
"cds_start": -4,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 620,
"mane_select": "NM_000519.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBD",
"gene_hgnc_id": 4829,
"hgvs_c": "c.-118C>T",
"hgvs_p": null,
"transcript": "ENST00000292901.7",
"protein_id": "ENSP00000292901.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 141,
"cds_start": -4,
"cds_end": null,
"cds_length": 426,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 486,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBD",
"gene_hgnc_id": 4829,
"hgvs_c": "c.-118C>T",
"hgvs_p": null,
"transcript": "ENST00000417377.1",
"protein_id": "ENSP00000414741.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 84,
"cds_start": -4,
"cds_end": null,
"cds_length": 255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 305,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HBD",
"gene_hgnc_id": 4829,
"dbsnp": "rs549964658",
"frequency_reference_population": 0.0024746389,
"hom_count_reference_population": 36,
"allele_count_reference_population": 1952,
"gnomad_exomes_af": 0.0028829,
"gnomad_genomes_af": 0.000768271,
"gnomad_exomes_ac": 1835,
"gnomad_genomes_ac": 117,
"gnomad_exomes_homalt": 35,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6600000262260437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.942,
"phylop100way_prediction": "Benign",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP5,BP4,BS1_Supporting,BS2_Supporting",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 3,
"pathogenic_score": 1,
"criteria": [
"PP5",
"BP4",
"BS1_Supporting",
"BS2_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000643122.1",
"gene_symbol": "HBD",
"hgnc_id": 4829,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-28-90C>T",
"hgvs_p": null
},
{
"score": -5,
"benign_score": 6,
"pathogenic_score": 1,
"criteria": [
"PP5",
"BP4",
"BS1_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000759072.1",
"gene_symbol": "ENSG00000298932",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.266-8558G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Delta-beta-thalassemia,HBD-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 US:1",
"phenotype_combined": "not provided|Delta-beta-thalassemia|HBD-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}