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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: 10-13288428-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=13288428&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 13288428,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000263038.9",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.610G>A",
"hgvs_p": "p.Gly204Ser",
"transcript": "NM_006214.4",
"protein_id": "NP_006205.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 338,
"cds_start": 610,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 632,
"cdna_end": null,
"cdna_length": 1541,
"mane_select": "ENST00000263038.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.610G>A",
"hgvs_p": "p.Gly204Ser",
"transcript": "ENST00000263038.9",
"protein_id": "ENSP00000263038.4",
"transcript_support_level": 1,
"aa_start": 204,
"aa_end": null,
"aa_length": 338,
"cds_start": 610,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 632,
"cdna_end": null,
"cdna_length": 1541,
"mane_select": "NM_006214.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.616G>A",
"hgvs_p": "p.Gly206Ser",
"transcript": "NM_001323082.2",
"protein_id": "NP_001310011.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 340,
"cds_start": 616,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 1547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Gly187Ser",
"transcript": "ENST00000396920.7",
"protein_id": "ENSP00000380126.3",
"transcript_support_level": 5,
"aa_start": 187,
"aa_end": null,
"aa_length": 321,
"cds_start": 559,
"cds_end": null,
"cds_length": 966,
"cdna_start": 964,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Gly106Ser",
"transcript": "NM_001323084.2",
"protein_id": "NP_001310013.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 240,
"cds_start": 316,
"cds_end": null,
"cds_length": 723,
"cdna_start": 826,
"cdna_end": null,
"cdna_length": 1735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.310G>A",
"hgvs_p": "p.Gly104Ser",
"transcript": "NM_001037537.2",
"protein_id": "NP_001032626.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 238,
"cds_start": 310,
"cds_end": null,
"cds_length": 717,
"cdna_start": 820,
"cdna_end": null,
"cdna_length": 1729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.310G>A",
"hgvs_p": "p.Gly104Ser",
"transcript": "NM_001323080.2",
"protein_id": "NP_001310009.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 238,
"cds_start": 310,
"cds_end": null,
"cds_length": 717,
"cdna_start": 879,
"cdna_end": null,
"cdna_length": 1788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.310G>A",
"hgvs_p": "p.Gly104Ser",
"transcript": "ENST00000396913.6",
"protein_id": "ENSP00000380121.2",
"transcript_support_level": 5,
"aa_start": 104,
"aa_end": null,
"aa_length": 238,
"cds_start": 310,
"cds_end": null,
"cds_length": 717,
"cdna_start": 820,
"cdna_end": null,
"cdna_length": 1732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"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": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.616G>A",
"hgvs_p": "p.Gly206Ser",
"transcript": "ENST00000479604.1",
"protein_id": "ENSP00000420117.1",
"transcript_support_level": 3,
"aa_start": 206,
"aa_end": null,
"aa_length": 209,
"cds_start": 616,
"cds_end": null,
"cds_length": 632,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 642,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.310G>A",
"hgvs_p": "p.Gly104Ser",
"transcript": "ENST00000453759.6",
"protein_id": "ENSP00000412525.2",
"transcript_support_level": 5,
"aa_start": 104,
"aa_end": null,
"aa_length": 175,
"cds_start": 310,
"cds_end": null,
"cds_length": 528,
"cdna_start": 665,
"cdna_end": null,
"cdna_length": 883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.415-4589G>A",
"hgvs_p": null,
"transcript": "NM_001323083.2",
"protein_id": "NP_001310012.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 250,
"cds_start": -4,
"cds_end": null,
"cds_length": 753,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"dbsnp": "rs104894173",
"frequency_reference_population": 0.000016108506,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000171015,
"gnomad_genomes_af": 0.00000657047,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9938359260559082,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.948,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7722,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.56,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.074,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000263038.9",
"gene_symbol": "PHYH",
"hgnc_id": 8940,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.610G>A",
"hgvs_p": "p.Gly204Ser"
}
],
"clinvar_disease": " 1, ADULT,Phytanic acid storage disease,REFSUM DISEASE",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "REFSUM DISEASE, ADULT, 1|Phytanic acid storage disease",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}