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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: 11-34960466-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=34960466&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 34960466,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000227868.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.589C>A",
"hgvs_p": "p.Leu197Met",
"transcript": "NM_003477.3",
"protein_id": "NP_003468.2",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 501,
"cds_start": 589,
"cds_end": null,
"cds_length": 1506,
"cdna_start": 627,
"cdna_end": null,
"cdna_length": 2500,
"mane_select": "ENST00000227868.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.589C>A",
"hgvs_p": "p.Leu197Met",
"transcript": "ENST00000227868.9",
"protein_id": "ENSP00000227868.4",
"transcript_support_level": 1,
"aa_start": 197,
"aa_end": null,
"aa_length": 501,
"cds_start": 589,
"cds_end": null,
"cds_length": 1506,
"cdna_start": 627,
"cdna_end": null,
"cdna_length": 2500,
"mane_select": "NM_003477.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Met",
"transcript": "NM_001135024.2",
"protein_id": "NP_001128496.2",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 441,
"cds_start": 409,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 478,
"cdna_end": null,
"cdna_length": 2351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Met",
"transcript": "ENST00000448838.8",
"protein_id": "ENSP00000389404.3",
"transcript_support_level": 5,
"aa_start": 137,
"aa_end": null,
"aa_length": 441,
"cds_start": 409,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 786,
"cdna_end": null,
"cdna_length": 2659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.508C>A",
"hgvs_p": "p.Leu170Met",
"transcript": "ENST00000533262.1",
"protein_id": "ENSP00000432277.1",
"transcript_support_level": 4,
"aa_start": 170,
"aa_end": null,
"aa_length": 181,
"cds_start": 508,
"cds_end": null,
"cds_length": 546,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Met",
"transcript": "ENST00000533550.5",
"protein_id": "ENSP00000431281.1",
"transcript_support_level": 4,
"aa_start": 137,
"aa_end": null,
"aa_length": 150,
"cds_start": 409,
"cds_end": null,
"cds_length": 454,
"cdna_start": 539,
"cdna_end": null,
"cdna_length": 584,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Met",
"transcript": "XM_011520390.2",
"protein_id": "XP_011518692.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 441,
"cds_start": 409,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 448,
"cdna_end": null,
"cdna_length": 2321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.342+12860C>A",
"hgvs_p": null,
"transcript": "NM_001166158.2",
"protein_id": "NP_001159630.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 274,
"cds_start": -4,
"cds_end": null,
"cds_length": 825,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.342+12860C>A",
"hgvs_p": null,
"transcript": "ENST00000430469.6",
"protein_id": "ENSP00000415695.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 274,
"cds_start": -4,
"cds_end": null,
"cds_length": 825,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"dbsnp": "rs139052284",
"frequency_reference_population": 0.00022125676,
"hom_count_reference_population": 1,
"allele_count_reference_population": 357,
"gnomad_exomes_af": 0.000112917,
"gnomad_genomes_af": 0.00126098,
"gnomad_exomes_ac": 165,
"gnomad_genomes_ac": 192,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009708434343338013,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.275,
"revel_prediction": "Benign",
"alphamissense_score": 0.1309,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.344,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000227868.9",
"gene_symbol": "PDHX",
"hgnc_id": 21350,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.589C>A",
"hgvs_p": "p.Leu197Met"
}
],
"clinvar_disease": "Pyruvate dehydrogenase E3-binding protein deficiency,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 LB:2",
"phenotype_combined": "not provided|Pyruvate dehydrogenase E3-binding protein deficiency|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}