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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: X-24527621-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=24527621&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 24527621,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000379162.9",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK3",
"gene_hgnc_id": 8811,
"hgvs_c": "c.798C>A",
"hgvs_p": "p.Gly266Gly",
"transcript": "NM_005391.5",
"protein_id": "NP_005382.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 406,
"cds_start": 798,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 968,
"cdna_end": null,
"cdna_length": 1741,
"mane_select": "ENST00000379162.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK3",
"gene_hgnc_id": 8811,
"hgvs_c": "c.798C>A",
"hgvs_p": "p.Gly266Gly",
"transcript": "ENST00000379162.9",
"protein_id": "ENSP00000368460.4",
"transcript_support_level": 1,
"aa_start": 266,
"aa_end": null,
"aa_length": 406,
"cds_start": 798,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 968,
"cdna_end": null,
"cdna_length": 1741,
"mane_select": "NM_005391.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK3",
"gene_hgnc_id": 8811,
"hgvs_c": "c.798C>A",
"hgvs_p": "p.Gly266Gly",
"transcript": "NM_001142386.3",
"protein_id": "NP_001135858.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 415,
"cds_start": 798,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 968,
"cdna_end": null,
"cdna_length": 12720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK3",
"gene_hgnc_id": 8811,
"hgvs_c": "c.798C>A",
"hgvs_p": "p.Gly266Gly",
"transcript": "ENST00000568479.2",
"protein_id": "ENSP00000498864.1",
"transcript_support_level": 6,
"aa_start": 266,
"aa_end": null,
"aa_length": 415,
"cds_start": 798,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 968,
"cdna_end": null,
"cdna_length": 12720,
"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": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK3",
"gene_hgnc_id": 8811,
"hgvs_c": "n.798C>A",
"hgvs_p": null,
"transcript": "ENST00000648777.1",
"protein_id": "ENSP00000497727.1",
"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": 4720,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK3",
"gene_hgnc_id": 8811,
"hgvs_c": "n.926C>A",
"hgvs_p": null,
"transcript": "ENST00000688031.1",
"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": 2005,
"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": "PDK3",
"gene_hgnc_id": 8811,
"hgvs_c": "n.2140C>A",
"hgvs_p": null,
"transcript": "ENST00000688551.1",
"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": 3983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDK3",
"gene_hgnc_id": 8811,
"dbsnp": "rs1250656724",
"frequency_reference_population": 0.000010046179,
"hom_count_reference_population": 2,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.0000101623,
"gnomad_genomes_af": 0.00000892443,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.38999998569488525,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.245,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000379162.9",
"gene_symbol": "PDK3",
"hgnc_id": 8811,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.798C>A",
"hgvs_p": "p.Gly266Gly"
}
],
"clinvar_disease": "Charcot-Marie-Tooth disease X-linked dominant 6,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "Charcot-Marie-Tooth disease X-linked dominant 6|not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}