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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: 22-30579758-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=30579758&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 30579758,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000354694.12",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.1347G>T",
"hgvs_p": "p.Glu449Asp",
"transcript": "NM_014303.4",
"protein_id": "NP_055118.1",
"transcript_support_level": null,
"aa_start": 449,
"aa_end": null,
"aa_length": 588,
"cds_start": 1347,
"cds_end": null,
"cds_length": 1767,
"cdna_start": 1424,
"cdna_end": null,
"cdna_length": 2265,
"mane_select": "ENST00000354694.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.1347G>T",
"hgvs_p": "p.Glu449Asp",
"transcript": "ENST00000354694.12",
"protein_id": "ENSP00000346725.6",
"transcript_support_level": 1,
"aa_start": 449,
"aa_end": null,
"aa_length": 588,
"cds_start": 1347,
"cds_end": null,
"cds_length": 1767,
"cdna_start": 1424,
"cdna_end": null,
"cdna_length": 2265,
"mane_select": "NM_014303.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.1332G>T",
"hgvs_p": "p.Glu444Asp",
"transcript": "ENST00000335214.8",
"protein_id": "ENSP00000334612.6",
"transcript_support_level": 1,
"aa_start": 444,
"aa_end": null,
"aa_length": 583,
"cds_start": 1332,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 1357,
"cdna_end": null,
"cdna_length": 1988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.1332G>T",
"hgvs_p": "p.Glu444Asp",
"transcript": "NM_001243225.2",
"protein_id": "NP_001230154.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 583,
"cds_start": 1332,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 1409,
"cdna_end": null,
"cdna_length": 2250,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.1296G>T",
"hgvs_p": "p.Glu432Asp",
"transcript": "ENST00000402284.7",
"protein_id": "ENSP00000384252.3",
"transcript_support_level": 5,
"aa_start": 432,
"aa_end": null,
"aa_length": 571,
"cds_start": 1296,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 1343,
"cdna_end": null,
"cdna_length": 2144,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.930G>T",
"hgvs_p": "p.Glu310Asp",
"transcript": "NM_001282327.1",
"protein_id": "NP_001269256.1",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 449,
"cds_start": 930,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1852,
"cdna_end": null,
"cdna_length": 2693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.930G>T",
"hgvs_p": "p.Glu310Asp",
"transcript": "NM_001282328.1",
"protein_id": "NP_001269257.1",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 449,
"cds_start": 930,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1899,
"cdna_end": null,
"cdna_length": 2740,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.930G>T",
"hgvs_p": "p.Glu310Asp",
"transcript": "ENST00000402281.5",
"protein_id": "ENSP00000384366.1",
"transcript_support_level": 2,
"aa_start": 310,
"aa_end": null,
"aa_length": 449,
"cds_start": 930,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1922,
"cdna_end": null,
"cdna_length": 2760,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.930G>T",
"hgvs_p": "p.Glu310Asp",
"transcript": "ENST00000405677.5",
"protein_id": "ENSP00000385654.1",
"transcript_support_level": 2,
"aa_start": 310,
"aa_end": null,
"aa_length": 449,
"cds_start": 930,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1874,
"cdna_end": null,
"cdna_length": 2708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "c.165G>T",
"hgvs_p": "p.Glu55Asp",
"transcript": "ENST00000441668.5",
"protein_id": "ENSP00000404234.1",
"transcript_support_level": 3,
"aa_start": 55,
"aa_end": null,
"aa_length": 193,
"cds_start": 165,
"cds_end": null,
"cds_length": 582,
"cdna_start": 166,
"cdna_end": null,
"cdna_length": 999,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"hgvs_c": "n.317G>T",
"hgvs_p": null,
"transcript": "ENST00000488719.1",
"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": 1732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PES1",
"gene_hgnc_id": 8848,
"dbsnp": "rs139824084",
"frequency_reference_population": 0.000033460485,
"hom_count_reference_population": 0,
"allele_count_reference_population": 54,
"gnomad_exomes_af": 0.0000150527,
"gnomad_genomes_af": 0.000210095,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 32,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0613955557346344,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.078,
"revel_prediction": "Benign",
"alphamissense_score": 0.1573,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.401,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000354694.12",
"gene_symbol": "PES1",
"hgnc_id": 8848,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1347G>T",
"hgvs_p": "p.Glu449Asp"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}