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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: 19-14053733-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=14053733&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 14053733,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001145028.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PALM3",
"gene_hgnc_id": 33274,
"hgvs_c": "c.1939G>A",
"hgvs_p": "p.Ala647Thr",
"transcript": "NM_001145028.2",
"protein_id": "NP_001138500.2",
"transcript_support_level": null,
"aa_start": 647,
"aa_end": null,
"aa_length": 688,
"cds_start": 1939,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000669674.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145028.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PALM3",
"gene_hgnc_id": 33274,
"hgvs_c": "c.1939G>A",
"hgvs_p": "p.Ala647Thr",
"transcript": "ENST00000669674.2",
"protein_id": "ENSP00000499271.1",
"transcript_support_level": null,
"aa_start": 647,
"aa_end": null,
"aa_length": 688,
"cds_start": 1939,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001145028.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000669674.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PALM3",
"gene_hgnc_id": 33274,
"hgvs_c": "c.1819G>A",
"hgvs_p": "p.Ala607Thr",
"transcript": "ENST00000661591.1",
"protein_id": "ENSP00000499248.1",
"transcript_support_level": null,
"aa_start": 607,
"aa_end": null,
"aa_length": 648,
"cds_start": 1819,
"cds_end": null,
"cds_length": 1947,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000661591.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PALM3",
"gene_hgnc_id": 33274,
"hgvs_c": "c.1741G>A",
"hgvs_p": "p.Ala581Thr",
"transcript": "NM_001367327.1",
"protein_id": "NP_001354256.1",
"transcript_support_level": null,
"aa_start": 581,
"aa_end": null,
"aa_length": 622,
"cds_start": 1741,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001367327.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PALM3",
"gene_hgnc_id": 33274,
"hgvs_c": "c.1741G>A",
"hgvs_p": "p.Ala581Thr",
"transcript": "ENST00000589048.2",
"protein_id": "ENSP00000465701.2",
"transcript_support_level": 3,
"aa_start": 581,
"aa_end": null,
"aa_length": 622,
"cds_start": 1741,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000589048.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PALM3",
"gene_hgnc_id": 33274,
"hgvs_c": "c.1858G>A",
"hgvs_p": "p.Ala620Thr",
"transcript": "XM_047438763.1",
"protein_id": "XP_047294719.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 661,
"cds_start": 1858,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438763.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PALM3",
"gene_hgnc_id": 33274,
"hgvs_c": "c.1741G>A",
"hgvs_p": "p.Ala581Thr",
"transcript": "XM_047438764.1",
"protein_id": "XP_047294720.1",
"transcript_support_level": null,
"aa_start": 581,
"aa_end": null,
"aa_length": 622,
"cds_start": 1741,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438764.1"
}
],
"gene_symbol": "PALM3",
"gene_hgnc_id": 33274,
"dbsnp": "rs369857742",
"frequency_reference_population": 0.000085647895,
"hom_count_reference_population": 0,
"allele_count_reference_population": 131,
"gnomad_exomes_af": 0.0000878491,
"gnomad_genomes_af": 0.000065722,
"gnomad_exomes_ac": 121,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.048377424478530884,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.023,
"revel_prediction": "Benign",
"alphamissense_score": 0.0826,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.105,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001145028.2",
"gene_symbol": "PALM3",
"hgnc_id": 33274,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1939G>A",
"hgvs_p": "p.Ala647Thr"
}
],
"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
}