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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: 4-88067937-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=88067937&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 88067937,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000237596.7",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.2398A>G",
"hgvs_p": "p.Met800Val",
"transcript": "NM_000297.4",
"protein_id": "NP_000288.1",
"transcript_support_level": null,
"aa_start": 800,
"aa_end": null,
"aa_length": 968,
"cds_start": 2398,
"cds_end": null,
"cds_length": 2907,
"cdna_start": 2497,
"cdna_end": null,
"cdna_length": 5089,
"mane_select": "ENST00000237596.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.2398A>G",
"hgvs_p": "p.Met800Val",
"transcript": "ENST00000237596.7",
"protein_id": "ENSP00000237596.2",
"transcript_support_level": 1,
"aa_start": 800,
"aa_end": null,
"aa_length": 968,
"cds_start": 2398,
"cds_end": null,
"cds_length": 2907,
"cdna_start": 2497,
"cdna_end": null,
"cdna_length": 5089,
"mane_select": "NM_000297.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.2173A>G",
"hgvs_p": "p.Met725Val",
"transcript": "NM_001440544.1",
"protein_id": "NP_001427473.1",
"transcript_support_level": null,
"aa_start": 725,
"aa_end": null,
"aa_length": 893,
"cds_start": 2173,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 2272,
"cdna_end": null,
"cdna_length": 4864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.652A>G",
"hgvs_p": "p.Met218Val",
"transcript": "ENST00000502363.1",
"protein_id": "ENSP00000425289.1",
"transcript_support_level": 5,
"aa_start": 218,
"aa_end": null,
"aa_length": 386,
"cds_start": 652,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 1222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.652A>G",
"hgvs_p": "p.Met218Val",
"transcript": "ENST00000508588.5",
"protein_id": "ENSP00000427131.1",
"transcript_support_level": 2,
"aa_start": 218,
"aa_end": null,
"aa_length": 386,
"cds_start": 652,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 1047,
"cdna_end": null,
"cdna_length": 1720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1678A>G",
"hgvs_p": "p.Met560Val",
"transcript": "XM_011532029.2",
"protein_id": "XP_011530331.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 728,
"cds_start": 1678,
"cds_end": null,
"cds_length": 2187,
"cdna_start": 1775,
"cdna_end": null,
"cdna_length": 4367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1558A>G",
"hgvs_p": "p.Met520Val",
"transcript": "XM_011532030.3",
"protein_id": "XP_011530332.1",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 688,
"cds_start": 1558,
"cds_end": null,
"cds_length": 2067,
"cdna_start": 1817,
"cdna_end": null,
"cdna_length": 4409,
"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": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.650A>G",
"hgvs_p": null,
"transcript": "ENST00000511337.5",
"protein_id": null,
"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": 1362,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.876A>G",
"hgvs_p": null,
"transcript": "ENST00000512858.1",
"protein_id": null,
"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": 1554,
"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": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.2376A>G",
"hgvs_p": null,
"transcript": "NR_156488.2",
"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": 4968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"dbsnp": "rs2234917",
"frequency_reference_population": 0.0000020522475,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205225,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10115578770637512,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.05,
"revel_prediction": "Benign",
"alphamissense_score": 0.0621,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.488,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000237596.7",
"gene_symbol": "PKD2",
"hgnc_id": 9009,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2398A>G",
"hgvs_p": "p.Met800Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}