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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: 5-254492-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=254492&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 254492,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000264932.11",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.1894G>A",
"hgvs_p": "p.Val632Ile",
"transcript": "NM_004168.4",
"protein_id": "NP_004159.2",
"transcript_support_level": null,
"aa_start": 632,
"aa_end": null,
"aa_length": 664,
"cds_start": 1894,
"cds_end": null,
"cds_length": 1995,
"cdna_start": 1930,
"cdna_end": null,
"cdna_length": 2693,
"mane_select": "ENST00000264932.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.1894G>A",
"hgvs_p": "p.Val632Ile",
"transcript": "ENST00000264932.11",
"protein_id": "ENSP00000264932.6",
"transcript_support_level": 1,
"aa_start": 632,
"aa_end": null,
"aa_length": 664,
"cds_start": 1894,
"cds_end": null,
"cds_length": 1995,
"cdna_start": 1930,
"cdna_end": null,
"cdna_length": 2693,
"mane_select": "NM_004168.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286001",
"gene_hgnc_id": null,
"hgvs_c": "n.*627G>A",
"hgvs_p": null,
"transcript": "ENST00000651543.1",
"protein_id": "ENSP00000499215.1",
"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": 3665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286001",
"gene_hgnc_id": null,
"hgvs_c": "n.*627G>A",
"hgvs_p": null,
"transcript": "ENST00000651543.1",
"protein_id": "ENSP00000499215.1",
"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": 3665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Val584Ile",
"transcript": "NM_001294332.2",
"protein_id": "NP_001281261.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 616,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1786,
"cdna_end": null,
"cdna_length": 2549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Val584Ile",
"transcript": "ENST00000510361.5",
"protein_id": "ENSP00000427703.1",
"transcript_support_level": 2,
"aa_start": 584,
"aa_end": null,
"aa_length": 616,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1788,
"cdna_end": null,
"cdna_length": 2148,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.1651G>A",
"hgvs_p": "p.Val551Ile",
"transcript": "NM_001330758.2",
"protein_id": "NP_001317687.1",
"transcript_support_level": null,
"aa_start": 551,
"aa_end": null,
"aa_length": 583,
"cds_start": 1651,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 1687,
"cdna_end": null,
"cdna_length": 2450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.1651G>A",
"hgvs_p": "p.Val551Ile",
"transcript": "ENST00000504309.5",
"protein_id": "ENSP00000426514.1",
"transcript_support_level": 5,
"aa_start": 551,
"aa_end": null,
"aa_length": 583,
"cds_start": 1651,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 1704,
"cdna_end": null,
"cdna_length": 2067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.1894G>A",
"hgvs_p": "p.Val632Ile",
"transcript": "XM_011514072.3",
"protein_id": "XP_011512374.1",
"transcript_support_level": null,
"aa_start": 632,
"aa_end": null,
"aa_length": 680,
"cds_start": 1894,
"cds_end": null,
"cds_length": 2043,
"cdna_start": 1930,
"cdna_end": null,
"cdna_length": 2926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Val584Ile",
"transcript": "XM_047417467.1",
"protein_id": "XP_047273423.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 632,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1786,
"cdna_end": null,
"cdna_length": 2782,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.1651G>A",
"hgvs_p": "p.Val551Ile",
"transcript": "XM_011514073.3",
"protein_id": "XP_011512375.1",
"transcript_support_level": null,
"aa_start": 551,
"aa_end": null,
"aa_length": 599,
"cds_start": 1651,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1687,
"cdna_end": null,
"cdna_length": 2683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.339G>A",
"hgvs_p": "p.Thr113Thr",
"transcript": "ENST00000515815.5",
"protein_id": "ENSP00000422404.1",
"transcript_support_level": 3,
"aa_start": 113,
"aa_end": null,
"aa_length": 125,
"cds_start": 339,
"cds_end": null,
"cds_length": 378,
"cdna_start": 341,
"cdna_end": null,
"cdna_length": 704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "c.267G>A",
"hgvs_p": "p.Thr89Thr",
"transcript": "ENST00000509564.1",
"protein_id": "ENSP00000421911.1",
"transcript_support_level": 3,
"aa_start": 89,
"aa_end": null,
"aa_length": 101,
"cds_start": 267,
"cds_end": null,
"cds_length": 306,
"cdna_start": 267,
"cdna_end": null,
"cdna_length": 630,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "n.2066G>A",
"hgvs_p": null,
"transcript": "ENST00000503674.5",
"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": 2426,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "n.301G>A",
"hgvs_p": null,
"transcript": "ENST00000507522.1",
"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": 644,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "n.2641G>A",
"hgvs_p": null,
"transcript": "ENST00000511810.5",
"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": 3001,
"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": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "n.1849G>A",
"hgvs_p": null,
"transcript": "ENST00000514027.5",
"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": 2209,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "n.1480G>A",
"hgvs_p": null,
"transcript": "ENST00000515752.5",
"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": 1809,
"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": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "n.1930G>A",
"hgvs_p": null,
"transcript": "XR_007058614.1",
"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": 6874,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"hgvs_c": "n.86-1842G>A",
"hgvs_p": null,
"transcript": "ENST00000509082.1",
"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": 434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SDHA",
"gene_hgnc_id": 10680,
"dbsnp": "rs369639811",
"frequency_reference_population": 0.000013387069,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.000013406,
"gnomad_genomes_af": 0.00001321,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06654724478721619,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.163,
"revel_prediction": "Benign",
"alphamissense_score": 0.0674,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.325,
"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": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000264932.11",
"gene_symbol": "SDHA",
"hgnc_id": 10680,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1894G>A",
"hgvs_p": "p.Val632Ile"
},
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000651543.1",
"gene_symbol": "ENSG00000286001",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*627G>A",
"hgvs_p": null
}
],
"clinvar_disease": " nuclear type 1,Hereditary cancer-predisposing syndrome,Mitochondrial complex II deficiency,Pheochromocytoma/paraganglioma syndrome 5",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Mitochondrial complex II deficiency, nuclear type 1;Pheochromocytoma/paraganglioma syndrome 5|Hereditary cancer-predisposing syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}