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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: 19-43496905-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=43496905&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 43496905,
"ref": "T",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000292140.10",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.*198A>T",
"hgvs_p": null,
"transcript": "ENST00000599242.1",
"protein_id": "ENSP00000471158.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 279,
"cds_start": -4,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2286,
"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": 16,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.825+213A>T",
"hgvs_p": null,
"transcript": "NM_198850.4",
"protein_id": "NP_942147.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 640,
"cds_start": -4,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2402,
"mane_select": "ENST00000292140.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.825+213A>T",
"hgvs_p": null,
"transcript": "ENST00000292140.10",
"protein_id": "ENSP00000292140.5",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 640,
"cds_start": -4,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2402,
"mane_select": "NM_198850.4",
"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": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.243+213A>T",
"hgvs_p": null,
"transcript": "ENST00000600660.1",
"protein_id": "ENSP00000473000.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 231,
"cds_start": -4,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "n.825+213A>T",
"hgvs_p": null,
"transcript": "ENST00000596141.2",
"protein_id": "ENSP00000469372.2",
"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": 3188,
"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": 16,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.825+213A>T",
"hgvs_p": null,
"transcript": "XM_005259169.5",
"protein_id": "XP_005259226.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 635,
"cds_start": -4,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2387,
"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": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.825+213A>T",
"hgvs_p": null,
"transcript": "XM_047439240.1",
"protein_id": "XP_047295196.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 635,
"cds_start": -4,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2245,
"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": 16,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.825+213A>T",
"hgvs_p": null,
"transcript": "XM_005259170.5",
"protein_id": "XP_005259227.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 601,
"cds_start": -4,
"cds_end": null,
"cds_length": 1806,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2285,
"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": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.825+213A>T",
"hgvs_p": null,
"transcript": "XM_047439241.1",
"protein_id": "XP_047295197.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 601,
"cds_start": -4,
"cds_end": null,
"cds_length": 1806,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2143,
"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": 14,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.825+213A>T",
"hgvs_p": null,
"transcript": "XM_005259171.5",
"protein_id": "XP_005259228.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 538,
"cds_start": -4,
"cds_end": null,
"cds_length": 1617,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2257,
"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": 11,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"hgvs_c": "c.825+213A>T",
"hgvs_p": null,
"transcript": "XM_047439242.1",
"protein_id": "XP_047295198.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 401,
"cds_start": -4,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1485,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHLDB3",
"gene_hgnc_id": 30499,
"dbsnp": "rs2682547",
"frequency_reference_population": 0.0000017905039,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 0.0000017905,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9100000262260437,
"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": -0.91,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.655,
"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": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000292140.10",
"gene_symbol": "PHLDB3",
"hgnc_id": 30499,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.825+213A>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}