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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: 6-28297909-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=28297909&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 28297909,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_032507.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.787A>G",
"hgvs_p": "p.Thr263Ala",
"transcript": "NM_032507.4",
"protein_id": "NP_115896.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 809,
"cds_start": 787,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 1172,
"cdna_end": null,
"cdna_length": 3080,
"mane_select": "ENST00000682144.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.787A>G",
"hgvs_p": "p.Thr263Ala",
"transcript": "ENST00000682144.1",
"protein_id": "ENSP00000506997.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 809,
"cds_start": 787,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 1172,
"cdna_end": null,
"cdna_length": 3080,
"mane_select": "NM_032507.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.787A>G",
"hgvs_p": "p.Thr263Ala",
"transcript": "ENST00000259883.3",
"protein_id": "ENSP00000259883.3",
"transcript_support_level": 1,
"aa_start": 263,
"aa_end": null,
"aa_length": 809,
"cds_start": 787,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 1192,
"cdna_end": null,
"cdna_length": 3100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.787A>G",
"hgvs_p": "p.Thr263Ala",
"transcript": "NM_001184743.2",
"protein_id": "NP_001171672.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 809,
"cds_start": 787,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 1192,
"cdna_end": null,
"cdna_length": 3100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "c.787A>G",
"hgvs_p": "p.Thr263Ala",
"transcript": "NM_001386059.1",
"protein_id": "NP_001372988.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 809,
"cds_start": 787,
"cds_end": null,
"cds_length": 2430,
"cdna_start": 959,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.1309A>G",
"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": 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.1035A>G",
"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": 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.1015A>G",
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.1185A>G",
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.1165A>G",
"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
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"hgvs_c": "n.1157+964A>G",
"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
}
],
"gene_symbol": "PGBD1",
"gene_hgnc_id": 19398,
"dbsnp": "rs757842321",
"frequency_reference_population": 0.000006587381,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000583729,
"gnomad_genomes_af": 0.0000135542,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0427490770816803,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.022,
"revel_prediction": "Benign",
"alphamissense_score": 0.0747,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.582,
"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": "NM_032507.4",
"gene_symbol": "PGBD1",
"hgnc_id": 19398,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.787A>G",
"hgvs_p": "p.Thr263Ala"
}
],
"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
}