← Back to variant description
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-22227526-A-ATGAC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=22227526&ref=A&alt=ATGAC&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"frameshift_variant",
"stop_gained"
],
"gene_symbol": "PHEX",
"hgnc_id": 8918,
"hgvs_c": "c.1986_1989dupTGAC",
"hgvs_p": "p.Arg664fs",
"inheritance_mode": "XL",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000444.6",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "PTCHD1-AS",
"hgnc_id": 37703,
"hgvs_c": "n.988_991dupGTCA",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 10,
"score": 10,
"transcript": "NR_073010.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "ATGAC",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "X",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Familial X-linked hypophosphatemic vitamin D refractory rickets,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "*Q?",
"aa_end": null,
"aa_length": 749,
"aa_ref": "R",
"aa_start": 664,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6288,
"cdna_start": 2671,
"cds_end": null,
"cds_length": 2250,
"cds_start": 1990,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_000444.6",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "c.1986_1989dupTGAC",
"hgvs_p": "p.Arg664fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000379374.5",
"protein_coding": true,
"protein_id": "NP_000435.3",
"strand": true,
"transcript": "NM_000444.6",
"transcript_support_level": null
},
{
"aa_alt": "*Q?",
"aa_end": null,
"aa_length": 749,
"aa_ref": "R",
"aa_start": 664,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6288,
"cdna_start": 2671,
"cds_end": null,
"cds_length": 2250,
"cds_start": 1990,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000379374.5",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "c.1986_1989dupTGAC",
"hgvs_p": "p.Arg664fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000444.6",
"protein_coding": true,
"protein_id": "ENSP00000368682.4",
"strand": true,
"transcript": "ENST00000379374.5",
"transcript_support_level": 1
},
{
"aa_alt": "*Q?",
"aa_end": null,
"aa_length": 695,
"aa_ref": "R",
"aa_start": 664,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6211,
"cdna_start": 2671,
"cds_end": null,
"cds_length": 2088,
"cds_start": 1990,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 21,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001282754.2",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "c.1986_1989dupTGAC",
"hgvs_p": "p.Arg664fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001269683.1",
"strand": true,
"transcript": "NM_001282754.2",
"transcript_support_level": null
},
{
"aa_alt": "*Q?",
"aa_end": null,
"aa_length": 267,
"aa_ref": "R",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2128,
"cdna_start": 822,
"cds_end": null,
"cds_length": 804,
"cds_start": 544,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000684356.1",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "c.540_543dupTGAC",
"hgvs_p": "p.Arg182fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000507619.1",
"strand": true,
"transcript": "ENST00000684356.1",
"transcript_support_level": null
},
{
"aa_alt": "*Q?",
"aa_end": null,
"aa_length": 652,
"aa_ref": "R",
"aa_start": 567,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5729,
"cdna_start": 2112,
"cds_end": null,
"cds_length": 1959,
"cds_start": 1699,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_024452390.2",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "c.1695_1698dupTGAC",
"hgvs_p": "p.Arg567fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024308158.1",
"strand": true,
"transcript": "XM_024452390.2",
"transcript_support_level": null
},
{
"aa_alt": "*Q?",
"aa_end": null,
"aa_length": 497,
"aa_ref": "R",
"aa_start": 412,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4978,
"cdna_start": 1361,
"cds_end": null,
"cds_length": 1494,
"cds_start": 1234,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_011545533.2",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "c.1230_1233dupTGAC",
"hgvs_p": "p.Arg412fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011543835.1",
"strand": true,
"transcript": "XM_011545533.2",
"transcript_support_level": null
},
{
"aa_alt": "*Q?",
"aa_end": null,
"aa_length": 497,
"aa_ref": "R",
"aa_start": 412,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4980,
"cdna_start": 1363,
"cds_end": null,
"cds_length": 1494,
"cds_start": 1234,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_017029579.2",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "c.1230_1233dupTGAC",
"hgvs_p": "p.Arg412fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016885068.1",
"strand": true,
"transcript": "XM_017029579.2",
"transcript_support_level": null
},
{
"aa_alt": "*Q?",
"aa_end": null,
"aa_length": 380,
"aa_ref": "R",
"aa_start": 295,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4998,
"cdna_start": 1381,
"cds_end": null,
"cds_length": 1143,
"cds_start": 883,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011545536.3",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "c.879_882dupTGAC",
"hgvs_p": "p.Arg295fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011543838.1",
"strand": true,
"transcript": "XM_011545536.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1443,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000669979.1",
"gene_hgnc_id": 37703,
"gene_symbol": "PTCHD1-AS",
"hgvs_c": "n.265_268dupGTCA",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000669979.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2495,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000683162.1",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "n.540_543dupTGAC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508059.1",
"strand": true,
"transcript": "ENST00000683162.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2159,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000683289.1",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "n.540_543dupTGAC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508195.1",
"strand": true,
"transcript": "ENST00000683289.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1262,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000683917.1",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "n.770_773dupTGAC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000683917.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2332,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000684745.1",
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"hgvs_c": "n.1660_1663dupTGAC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000684745.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1141,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000687248.2",
"gene_hgnc_id": 37703,
"gene_symbol": "PTCHD1-AS",
"hgvs_c": "n.1016_1019dupGTCA",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000687248.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1321,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000715857.1",
"gene_hgnc_id": 37703,
"gene_symbol": "PTCHD1-AS",
"hgvs_c": "n.417_420dupGTCA",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000715857.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1151,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000825156.1",
"gene_hgnc_id": 37703,
"gene_symbol": "PTCHD1-AS",
"hgvs_c": "n.447_450dupGTCA",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000825156.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3772,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NR_073010.2",
"gene_hgnc_id": 37703,
"gene_symbol": "PTCHD1-AS",
"hgvs_c": "n.988_991dupGTCA",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_073010.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 626,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000825157.1",
"gene_hgnc_id": 37703,
"gene_symbol": "PTCHD1-AS",
"hgvs_c": "n.309+26409_309+26412dupGTCA",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000825157.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1556151137",
"effect": "frameshift_variant,stop_gained",
"frequency_reference_population": null,
"gene_hgnc_id": 8918,
"gene_symbol": "PHEX",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Familial X-linked hypophosphatemic vitamin D refractory rickets|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.372,
"pos": 22227526,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_000444.6"
}
]
}