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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-22219070-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=22219070&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 22219070,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000379374.5",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.1735G>A",
"hgvs_p": "p.Gly579Arg",
"transcript": "NM_000444.6",
"protein_id": "NP_000435.3",
"transcript_support_level": null,
"aa_start": 579,
"aa_end": null,
"aa_length": 749,
"cds_start": 1735,
"cds_end": null,
"cds_length": 2250,
"cdna_start": 2416,
"cdna_end": null,
"cdna_length": 6288,
"mane_select": "ENST00000379374.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.1735G>A",
"hgvs_p": "p.Gly579Arg",
"transcript": "ENST00000379374.5",
"protein_id": "ENSP00000368682.4",
"transcript_support_level": 1,
"aa_start": 579,
"aa_end": null,
"aa_length": 749,
"cds_start": 1735,
"cds_end": null,
"cds_length": 2250,
"cdna_start": 2416,
"cdna_end": null,
"cdna_length": 6288,
"mane_select": "NM_000444.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.1735G>A",
"hgvs_p": "p.Gly579Arg",
"transcript": "NM_001282754.2",
"protein_id": "NP_001269683.1",
"transcript_support_level": null,
"aa_start": 579,
"aa_end": null,
"aa_length": 695,
"cds_start": 1735,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 2416,
"cdna_end": null,
"cdna_length": 6211,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.289G>A",
"hgvs_p": "p.Gly97Arg",
"transcript": "ENST00000684356.1",
"protein_id": "ENSP00000507619.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 267,
"cds_start": 289,
"cds_end": null,
"cds_length": 804,
"cdna_start": 567,
"cdna_end": null,
"cdna_length": 2128,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.289G>A",
"hgvs_p": "p.Gly97Arg",
"transcript": "ENST00000682888.1",
"protein_id": "ENSP00000508003.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 170,
"cds_start": 289,
"cds_end": null,
"cds_length": 515,
"cdna_start": 423,
"cdna_end": null,
"cdna_length": 653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.1444G>A",
"hgvs_p": "p.Gly482Arg",
"transcript": "XM_024452390.2",
"protein_id": "XP_024308158.1",
"transcript_support_level": null,
"aa_start": 482,
"aa_end": null,
"aa_length": 652,
"cds_start": 1444,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 1857,
"cdna_end": null,
"cdna_length": 5729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.979G>A",
"hgvs_p": "p.Gly327Arg",
"transcript": "XM_011545533.2",
"protein_id": "XP_011543835.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 497,
"cds_start": 979,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1106,
"cdna_end": null,
"cdna_length": 4978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.979G>A",
"hgvs_p": "p.Gly327Arg",
"transcript": "XM_017029579.2",
"protein_id": "XP_016885068.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 497,
"cds_start": 979,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 4980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "c.628G>A",
"hgvs_p": "p.Gly210Arg",
"transcript": "XM_011545536.3",
"protein_id": "XP_011543838.1",
"transcript_support_level": null,
"aa_start": 210,
"aa_end": null,
"aa_length": 380,
"cds_start": 628,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 1126,
"cdna_end": null,
"cdna_length": 4998,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "n.289G>A",
"hgvs_p": null,
"transcript": "ENST00000683162.1",
"protein_id": "ENSP00000508059.1",
"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": 2495,
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "n.289G>A",
"hgvs_p": null,
"transcript": "ENST00000683289.1",
"protein_id": "ENSP00000508195.1",
"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": 2159,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "n.519G>A",
"hgvs_p": null,
"transcript": "ENST00000683917.1",
"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": 1262,
"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": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"hgvs_c": "n.1409G>A",
"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": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTCHD1-AS",
"gene_hgnc_id": 37703,
"hgvs_c": "n.325+8400C>T",
"hgvs_p": null,
"transcript": "ENST00000669979.1",
"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": 1443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PTCHD1-AS",
"gene_hgnc_id": 37703,
"hgvs_c": "n.477+8400C>T",
"hgvs_p": null,
"transcript": "ENST00000715857.1",
"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": 1321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PTCHD1-AS",
"gene_hgnc_id": 37703,
"hgvs_c": "n.507+8400C>T",
"hgvs_p": null,
"transcript": "ENST00000825156.1",
"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": 1151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTCHD1-AS",
"gene_hgnc_id": 37703,
"hgvs_c": "n.310-29501C>T",
"hgvs_p": null,
"transcript": "ENST00000825157.1",
"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": 626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTCHD1-AS",
"gene_hgnc_id": 37703,
"hgvs_c": "n.1048+8400C>T",
"hgvs_p": null,
"transcript": "NR_073010.2",
"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": 3772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHEX",
"gene_hgnc_id": 8918,
"dbsnp": "rs875989883",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9948875904083252,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.49000000953674316,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.931,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9981,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.62,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.627,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.49,
"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": 23,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS1,PM1,PM2,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 23,
"benign_score": 0,
"pathogenic_score": 23,
"criteria": [
"PS1",
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000379374.5",
"gene_symbol": "PHEX",
"hgnc_id": 8918,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1735G>A",
"hgvs_p": "p.Gly579Arg"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NR_073010.2",
"gene_symbol": "PTCHD1-AS",
"hgnc_id": 37703,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1048+8400C>T",
"hgvs_p": null
}
],
"clinvar_disease": " type 2,Familial X-linked hypophosphatemic vitamin D refractory rickets,Vitamin D-dependent rickets,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:1",
"phenotype_combined": "Familial X-linked hypophosphatemic vitamin D refractory rickets|not provided|Vitamin D-dependent rickets, type 2",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}