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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: X-22090443-ACT-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=22090443&ref=ACT&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 22090443,
"ref": "ACT",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000379374.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.682_683delTC",
"hgvs_p": "p.Ser228fs",
"transcript": "NM_000444.6",
"protein_id": "NP_000435.3",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 749,
"cds_start": 682,
"cds_end": null,
"cds_length": 2250,
"cdna_start": 1363,
"cdna_end": null,
"cdna_length": 6288,
"mane_select": "ENST00000379374.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.682_683delTC",
"hgvs_p": "p.Ser228fs",
"transcript": "ENST00000379374.5",
"protein_id": "ENSP00000368682.4",
"transcript_support_level": 1,
"aa_start": 228,
"aa_end": null,
"aa_length": 749,
"cds_start": 682,
"cds_end": null,
"cds_length": 2250,
"cdna_start": 1363,
"cdna_end": null,
"cdna_length": 6288,
"mane_select": "NM_000444.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.682_683delTC",
"hgvs_p": "p.Ser228fs",
"transcript": "NM_001282754.2",
"protein_id": "NP_001269683.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 695,
"cds_start": 682,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1363,
"cdna_end": null,
"cdna_length": 6211,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.679_680delTC",
"hgvs_p": "p.Ser227fs",
"transcript": "ENST00000684143.1",
"protein_id": "ENSP00000508264.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 427,
"cds_start": 679,
"cds_end": null,
"cds_length": 1284,
"cdna_start": 1104,
"cdna_end": null,
"cdna_length": 1709,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.391_392delTC",
"hgvs_p": "p.Ser131fs",
"transcript": "XM_024452390.2",
"protein_id": "XP_024308158.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 652,
"cds_start": 391,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 804,
"cdna_end": null,
"cdna_length": 5729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.682_683delTC",
"hgvs_p": "p.Ser228fs",
"transcript": "XM_047442159.1",
"protein_id": "XP_047298115.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 475,
"cds_start": 682,
"cds_end": null,
"cds_length": 1428,
"cdna_start": 1363,
"cdna_end": null,
"cdna_length": 2241,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "n.1108_1109delTC",
"hgvs_p": null,
"transcript": "ENST00000475778.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 3222,
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "n.356_357delTC",
"hgvs_p": null,
"transcript": "ENST00000684745.1",
"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": 2332,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.-75_-74delTC",
"hgvs_p": null,
"transcript": "XM_011545533.2",
"protein_id": "XP_011543835.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 497,
"cds_start": -4,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.-75_-74delTC",
"hgvs_p": null,
"transcript": "XM_017029579.2",
"protein_id": "XP_016885068.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 497,
"cds_start": -4,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"dbsnp": "rs1064793956",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 6.086,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000379374.5",
"gene_symbol": "PHEX",
"hgnc_id": 8918,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.682_683delTC",
"hgvs_p": "p.Ser228fs"
}
],
"clinvar_disease": "Familial X-linked hypophosphatemic vitamin D refractory rickets,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "not provided|Familial X-linked hypophosphatemic vitamin D refractory rickets",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}