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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: 10-13283694-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=13283694&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 13283694,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000263038.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.824G>A",
"hgvs_p": "p.Arg275Gln",
"transcript": "NM_006214.4",
"protein_id": "NP_006205.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 338,
"cds_start": 824,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 846,
"cdna_end": null,
"cdna_length": 1541,
"mane_select": "ENST00000263038.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.824G>A",
"hgvs_p": "p.Arg275Gln",
"transcript": "ENST00000263038.9",
"protein_id": "ENSP00000263038.4",
"transcript_support_level": 1,
"aa_start": 275,
"aa_end": null,
"aa_length": 338,
"cds_start": 824,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 846,
"cdna_end": null,
"cdna_length": 1541,
"mane_select": "NM_006214.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.830G>A",
"hgvs_p": "p.Arg277Gln",
"transcript": "NM_001323082.2",
"protein_id": "NP_001310011.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 340,
"cds_start": 830,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 852,
"cdna_end": null,
"cdna_length": 1547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.773G>A",
"hgvs_p": "p.Arg258Gln",
"transcript": "ENST00000396920.7",
"protein_id": "ENSP00000380126.3",
"transcript_support_level": 5,
"aa_start": 258,
"aa_end": null,
"aa_length": 321,
"cds_start": 773,
"cds_end": null,
"cds_length": 966,
"cdna_start": 1178,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.560G>A",
"hgvs_p": "p.Arg187Gln",
"transcript": "NM_001323083.2",
"protein_id": "NP_001310012.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 250,
"cds_start": 560,
"cds_end": null,
"cds_length": 753,
"cdna_start": 582,
"cdna_end": null,
"cdna_length": 1277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.530G>A",
"hgvs_p": "p.Arg177Gln",
"transcript": "NM_001323084.2",
"protein_id": "NP_001310013.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 240,
"cds_start": 530,
"cds_end": null,
"cds_length": 723,
"cdna_start": 1040,
"cdna_end": null,
"cdna_length": 1735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.524G>A",
"hgvs_p": "p.Arg175Gln",
"transcript": "NM_001037537.2",
"protein_id": "NP_001032626.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 238,
"cds_start": 524,
"cds_end": null,
"cds_length": 717,
"cdna_start": 1034,
"cdna_end": null,
"cdna_length": 1729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.524G>A",
"hgvs_p": "p.Arg175Gln",
"transcript": "NM_001323080.2",
"protein_id": "NP_001310009.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 238,
"cds_start": 524,
"cds_end": null,
"cds_length": 717,
"cdna_start": 1093,
"cdna_end": null,
"cdna_length": 1788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.524G>A",
"hgvs_p": "p.Arg175Gln",
"transcript": "ENST00000396913.6",
"protein_id": "ENSP00000380121.2",
"transcript_support_level": 5,
"aa_start": 175,
"aa_end": null,
"aa_length": 238,
"cds_start": 524,
"cds_end": null,
"cds_length": 717,
"cdna_start": 1034,
"cdna_end": null,
"cdna_length": 1732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"hgvs_c": "c.524G>A",
"hgvs_p": "p.Arg175Gln",
"transcript": "ENST00000453759.6",
"protein_id": "ENSP00000412525.2",
"transcript_support_level": 5,
"aa_start": 175,
"aa_end": null,
"aa_length": 175,
"cds_start": 524,
"cds_end": null,
"cds_length": 528,
"cdna_start": 879,
"cdna_end": null,
"cdna_length": 883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"dbsnp": "rs104894174",
"frequency_reference_population": 0.000011152955,
"hom_count_reference_population": 0,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000102609,
"gnomad_genomes_af": 0.0000197283,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9858976602554321,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.942,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7824,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.51,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.024,
"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": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PM1",
"PM2",
"PM5",
"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.824G>A",
"hgvs_p": "p.Arg275Gln"
}
],
"clinvar_disease": " 1, ADULT,Phytanic acid storage disease,REFSUM DISEASE,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:2",
"phenotype_combined": "REFSUM DISEASE, ADULT, 1|not provided|Phytanic acid storage disease",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}