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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: 7-729774-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=729774&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 729774,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000297440.11",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF5",
"gene_hgnc_id": 26013,
"hgvs_c": "c.707A>T",
"hgvs_p": "p.His236Leu",
"transcript": "NM_017802.4",
"protein_id": "NP_060272.3",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 855,
"cds_start": 707,
"cds_end": null,
"cds_length": 2568,
"cdna_start": 729,
"cdna_end": null,
"cdna_length": 3412,
"mane_select": "ENST00000297440.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF5",
"gene_hgnc_id": 26013,
"hgvs_c": "c.707A>T",
"hgvs_p": "p.His236Leu",
"transcript": "ENST00000297440.11",
"protein_id": "ENSP00000297440.6",
"transcript_support_level": 1,
"aa_start": 236,
"aa_end": null,
"aa_length": 855,
"cds_start": 707,
"cds_end": null,
"cds_length": 2568,
"cdna_start": 729,
"cdna_end": null,
"cdna_length": 3412,
"mane_select": "NM_017802.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF5",
"gene_hgnc_id": 26013,
"hgvs_c": "c.110A>T",
"hgvs_p": "p.His37Leu",
"transcript": "ENST00000440747.5",
"protein_id": "ENSP00000403165.1",
"transcript_support_level": 2,
"aa_start": 37,
"aa_end": null,
"aa_length": 656,
"cds_start": 110,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 111,
"cdna_end": null,
"cdna_length": 2350,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF5",
"gene_hgnc_id": 26013,
"hgvs_c": "c.707A>T",
"hgvs_p": "p.His236Leu",
"transcript": "XM_024446813.2",
"protein_id": "XP_024302581.1",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 791,
"cds_start": 707,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 729,
"cdna_end": null,
"cdna_length": 3220,
"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": "DNAAF5",
"gene_hgnc_id": 26013,
"hgvs_c": "n.176A>T",
"hgvs_p": null,
"transcript": "ENST00000438961.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 579,
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAAF5",
"gene_hgnc_id": 26013,
"hgvs_c": "n.667A>T",
"hgvs_p": null,
"transcript": "NR_075098.2",
"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": 3350,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DNAAF5",
"gene_hgnc_id": 26013,
"hgvs_c": "c.96+2459A>T",
"hgvs_p": null,
"transcript": "ENST00000437419.5",
"protein_id": "ENSP00000410788.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": -4,
"cds_end": null,
"cds_length": 584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAAF5",
"gene_hgnc_id": 26013,
"dbsnp": "rs115058579",
"frequency_reference_population": 0.00026514847,
"hom_count_reference_population": 1,
"allele_count_reference_population": 428,
"gnomad_exomes_af": 0.000138863,
"gnomad_genomes_af": 0.00147721,
"gnomad_exomes_ac": 203,
"gnomad_genomes_ac": 225,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.010960638523101807,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.209,
"revel_prediction": "Benign",
"alphamissense_score": 0.0769,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.501,
"phylop100way_prediction": "Uncertain_significance",
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000297440.11",
"gene_symbol": "DNAAF5",
"hgnc_id": 26013,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.707A>T",
"hgvs_p": "p.His236Leu"
}
],
"clinvar_disease": "DNAAF5-related disorder,Primary ciliary dyskinesia,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "Primary ciliary dyskinesia|DNAAF5-related disorder|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}