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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: 17-47943335-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=47943335&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 47943335,
"ref": "T",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000642017.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "c.168T>G",
"hgvs_p": "p.Leu56Leu",
"transcript": "NM_018129.4",
"protein_id": "NP_060599.1",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 261,
"cds_start": 168,
"cds_end": null,
"cds_length": 786,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 3417,
"mane_select": "ENST00000642017.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "c.168T>G",
"hgvs_p": "p.Leu56Leu",
"transcript": "ENST00000642017.2",
"protein_id": "ENSP00000493302.2",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 261,
"cds_start": 168,
"cds_end": null,
"cds_length": 786,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 3417,
"mane_select": "NM_018129.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "c.168T>G",
"hgvs_p": "p.Leu56Leu",
"transcript": "ENST00000225573.5",
"protein_id": "ENSP00000225573.5",
"transcript_support_level": 1,
"aa_start": 56,
"aa_end": null,
"aa_length": 218,
"cds_start": 168,
"cds_end": null,
"cds_length": 657,
"cdna_start": 277,
"cdna_end": null,
"cdna_length": 2256,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "c.-73T>G",
"hgvs_p": null,
"transcript": "ENST00000583599.6",
"protein_id": "ENSP00000463919.2",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 164,
"cds_start": -4,
"cds_end": null,
"cds_length": 497,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "c.168T>G",
"hgvs_p": "p.Leu56Leu",
"transcript": "ENST00000434554.7",
"protein_id": "ENSP00000399960.3",
"transcript_support_level": 2,
"aa_start": 56,
"aa_end": null,
"aa_length": 243,
"cds_start": 168,
"cds_end": null,
"cds_length": 732,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 1196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "c.138T>G",
"hgvs_p": "p.Leu46Leu",
"transcript": "ENST00000584061.6",
"protein_id": "ENSP00000463972.2",
"transcript_support_level": 4,
"aa_start": 46,
"aa_end": null,
"aa_length": 238,
"cds_start": 138,
"cds_end": null,
"cds_length": 717,
"cdna_start": 138,
"cdna_end": null,
"cdna_length": 723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "c.168T>G",
"hgvs_p": "p.Leu56Leu",
"transcript": "NM_001436305.1",
"protein_id": "NP_001423234.1",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 218,
"cds_start": 168,
"cds_end": null,
"cds_length": 657,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 3288,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "c.81T>G",
"hgvs_p": "p.Leu27Leu",
"transcript": "ENST00000641511.1",
"protein_id": "ENSP00000493348.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 149,
"cds_start": 81,
"cds_end": null,
"cds_length": 451,
"cdna_start": 83,
"cdna_end": null,
"cdna_length": 453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.136T>G",
"hgvs_p": null,
"transcript": "ENST00000583245.6",
"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": 518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.243T>G",
"hgvs_p": null,
"transcript": "ENST00000641305.1",
"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": 3315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.*187T>G",
"hgvs_p": null,
"transcript": "ENST00000641323.1",
"protein_id": "ENSP00000492965.1",
"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": 3657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.168T>G",
"hgvs_p": null,
"transcript": "ENST00000641427.1",
"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": 1411,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "c.-73T>G",
"hgvs_p": null,
"transcript": "ENST00000583599.6",
"protein_id": "ENSP00000463919.2",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 164,
"cds_start": -4,
"cds_end": null,
"cds_length": 497,
"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": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.*187T>G",
"hgvs_p": null,
"transcript": "ENST00000641323.1",
"protein_id": "ENSP00000492965.1",
"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": 3657,
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.139-1281T>G",
"hgvs_p": null,
"transcript": "ENST00000582171.6",
"protein_id": "ENSP00000463994.1",
"transcript_support_level": 2,
"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": 1372,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.139-1281T>G",
"hgvs_p": null,
"transcript": "ENST00000585320.5",
"protein_id": "ENSP00000462345.1",
"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": 503,
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.44-1281T>G",
"hgvs_p": null,
"transcript": "ENST00000641285.1",
"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": 488,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.34-1281T>G",
"hgvs_p": null,
"transcript": "ENST00000641703.1",
"protein_id": "ENSP00000493219.1",
"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": 1131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.139-8T>G",
"hgvs_p": null,
"transcript": "ENST00000641709.1",
"protein_id": "ENSP00000493349.1",
"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": 3232,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"hgvs_c": "n.139-1281T>G",
"hgvs_p": null,
"transcript": "ENST00000641856.1",
"protein_id": "ENSP00000493224.1",
"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": 2619,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PNPO",
"gene_hgnc_id": 30260,
"dbsnp": "rs1060504669",
"frequency_reference_population": 0.00001970495,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.000019705,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5799999833106995,
"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": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.547,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000642017.2",
"gene_symbol": "PNPO",
"hgnc_id": 30260,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.168T>G",
"hgvs_p": "p.Leu56Leu"
}
],
"clinvar_disease": "PNPO-related disorder,Pyridoxal phosphate-responsive seizures",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Pyridoxal phosphate-responsive seizures|PNPO-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}