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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: 6-28296904-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=28296904&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 28296904,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000682144.1",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.731G>A",
"hgvs_p": "p.Gly244Glu",
"transcript": "NM_032507.4",
"protein_id": "NP_115896.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 809,
"cds_start": 731,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 1116,
"cdna_end": null,
"cdna_length": 3080,
"mane_select": "ENST00000682144.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.731G>A",
"hgvs_p": "p.Gly244Glu",
"transcript": "ENST00000682144.1",
"protein_id": "ENSP00000506997.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 809,
"cds_start": 731,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 1116,
"cdna_end": null,
"cdna_length": 3080,
"mane_select": "NM_032507.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.731G>A",
"hgvs_p": "p.Gly244Glu",
"transcript": "ENST00000259883.3",
"protein_id": "ENSP00000259883.3",
"transcript_support_level": 1,
"aa_start": 244,
"aa_end": null,
"aa_length": 809,
"cds_start": 731,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 1136,
"cdna_end": null,
"cdna_length": 3100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.731G>A",
"hgvs_p": "p.Gly244Glu",
"transcript": "NM_001184743.2",
"protein_id": "NP_001171672.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 809,
"cds_start": 731,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 1136,
"cdna_end": null,
"cdna_length": 3100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.731G>A",
"hgvs_p": "p.Gly244Glu",
"transcript": "NM_001386059.1",
"protein_id": "NP_001372988.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 809,
"cds_start": 731,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 2867,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.1116G>A",
"hgvs_p": null,
"transcript": "NR_169855.1",
"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": 3217,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.979G>A",
"hgvs_p": null,
"transcript": "NR_169856.1",
"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": 2943,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.959G>A",
"hgvs_p": null,
"transcript": "NR_169857.1",
"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": 2923,
"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": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.1129G>A",
"hgvs_p": null,
"transcript": "NR_169858.1",
"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": 3093,
"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": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.1116G>A",
"hgvs_p": null,
"transcript": "NR_169859.1",
"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": 2983,
"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": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.1109G>A",
"hgvs_p": null,
"transcript": "NR_169860.1",
"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": 3073,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"dbsnp": "rs3800324",
"frequency_reference_population": 0.06351812,
"hom_count_reference_population": 5597,
"allele_count_reference_population": 102518,
"gnomad_exomes_af": 0.0613183,
"gnomad_genomes_af": 0.0846417,
"gnomad_exomes_ac": 89633,
"gnomad_genomes_ac": 12885,
"gnomad_exomes_homalt": 4823,
"gnomad_genomes_homalt": 774,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004461318254470825,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.23000000417232513,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.071,
"revel_prediction": "Benign",
"alphamissense_score": 0.0677,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.074,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.23,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BA1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000682144.1",
"gene_symbol": "PGBD1",
"hgnc_id": 19398,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.731G>A",
"hgvs_p": "p.Gly244Glu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}