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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: 21-44521921-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=44521921&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "TSPEAR",
"hgnc_id": 1268,
"hgvs_c": "c.1528C>A",
"hgvs_p": "p.Arg510Arg",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_144991.3",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "TSPEAR-AS1",
"hgnc_id": 1271,
"hgvs_c": "n.217-3903G>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000465978.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_score": -3,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.61,
"chr": "21",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6100000143051147,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 669,
"aa_ref": "R",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3958,
"cdna_start": 1586,
"cds_end": null,
"cds_length": 2010,
"cds_start": 1528,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_144991.3",
"gene_hgnc_id": 1268,
"gene_symbol": "TSPEAR",
"hgvs_c": "c.1528C>A",
"hgvs_p": "p.Arg510Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000323084.9",
"protein_coding": true,
"protein_id": "NP_659428.2",
"strand": false,
"transcript": "NM_144991.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 669,
"aa_ref": "R",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3958,
"cdna_start": 1586,
"cds_end": null,
"cds_length": 2010,
"cds_start": 1528,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000323084.9",
"gene_hgnc_id": 1268,
"gene_symbol": "TSPEAR",
"hgvs_c": "c.1528C>A",
"hgvs_p": "p.Arg510Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_144991.3",
"protein_coding": true,
"protein_id": "ENSP00000321987.4",
"strand": false,
"transcript": "ENST00000323084.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2114,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000397916.1",
"gene_hgnc_id": 1268,
"gene_symbol": "TSPEAR",
"hgvs_c": "n.1483C>A",
"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": "ENST00000397916.1",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 711,
"aa_ref": "R",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3752,
"cdna_start": 1887,
"cds_end": null,
"cds_length": 2136,
"cds_start": 1528,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000943283.1",
"gene_hgnc_id": 1268,
"gene_symbol": "TSPEAR",
"hgvs_c": "c.1528C>A",
"hgvs_p": "p.Arg510Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000613342.1",
"strand": false,
"transcript": "ENST00000943283.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 601,
"aa_ref": "R",
"aa_start": 442,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4020,
"cdna_start": 1648,
"cds_end": null,
"cds_length": 1806,
"cds_start": 1324,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001272037.2",
"gene_hgnc_id": 1268,
"gene_symbol": "TSPEAR",
"hgvs_c": "c.1324C>A",
"hgvs_p": "p.Arg442Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001258966.1",
"strand": false,
"transcript": "NM_001272037.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2790,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000642437.1",
"gene_hgnc_id": 1268,
"gene_symbol": "TSPEAR",
"hgvs_c": "n.*1473C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000496535.1",
"strand": false,
"transcript": "ENST00000642437.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2790,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000642437.1",
"gene_hgnc_id": 1268,
"gene_symbol": "TSPEAR",
"hgvs_c": "n.*1473C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000496535.1",
"strand": false,
"transcript": "ENST00000642437.1",
"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": 345,
"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": "ENST00000465978.1",
"gene_hgnc_id": 1271,
"gene_symbol": "TSPEAR-AS1",
"hgvs_c": "n.217-3903G>T",
"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": "ENST00000465978.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201663789",
"effect": "synonymous_variant",
"frequency_reference_population": 6.841143e-7,
"gene_hgnc_id": 1268,
"gene_symbol": "TSPEAR",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84114e-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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.322,
"pos": 44521921,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_144991.3"
}
]
}