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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: 10-13283713-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=13283713&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 13283713,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000263038.9",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "H",
"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.805A>C",
"hgvs_p": "p.Asn269His",
"transcript": "NM_006214.4",
"protein_id": "NP_006205.1",
"transcript_support_level": null,
"aa_start": 269,
"aa_end": null,
"aa_length": 338,
"cds_start": 805,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 827,
"cdna_end": null,
"cdna_length": 1541,
"mane_select": "ENST00000263038.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"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.805A>C",
"hgvs_p": "p.Asn269His",
"transcript": "ENST00000263038.9",
"protein_id": "ENSP00000263038.4",
"transcript_support_level": 1,
"aa_start": 269,
"aa_end": null,
"aa_length": 338,
"cds_start": 805,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 827,
"cdna_end": null,
"cdna_length": 1541,
"mane_select": "NM_006214.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"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.811A>C",
"hgvs_p": "p.Asn271His",
"transcript": "NM_001323082.2",
"protein_id": "NP_001310011.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 340,
"cds_start": 811,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 833,
"cdna_end": null,
"cdna_length": 1547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"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.754A>C",
"hgvs_p": "p.Asn252His",
"transcript": "ENST00000396920.7",
"protein_id": "ENSP00000380126.3",
"transcript_support_level": 5,
"aa_start": 252,
"aa_end": null,
"aa_length": 321,
"cds_start": 754,
"cds_end": null,
"cds_length": 966,
"cdna_start": 1159,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"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.541A>C",
"hgvs_p": "p.Asn181His",
"transcript": "NM_001323083.2",
"protein_id": "NP_001310012.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 250,
"cds_start": 541,
"cds_end": null,
"cds_length": 753,
"cdna_start": 563,
"cdna_end": null,
"cdna_length": 1277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"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.511A>C",
"hgvs_p": "p.Asn171His",
"transcript": "NM_001323084.2",
"protein_id": "NP_001310013.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 240,
"cds_start": 511,
"cds_end": null,
"cds_length": 723,
"cdna_start": 1021,
"cdna_end": null,
"cdna_length": 1735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"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.505A>C",
"hgvs_p": "p.Asn169His",
"transcript": "NM_001037537.2",
"protein_id": "NP_001032626.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 238,
"cds_start": 505,
"cds_end": null,
"cds_length": 717,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 1729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"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.505A>C",
"hgvs_p": "p.Asn169His",
"transcript": "NM_001323080.2",
"protein_id": "NP_001310009.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 238,
"cds_start": 505,
"cds_end": null,
"cds_length": 717,
"cdna_start": 1074,
"cdna_end": null,
"cdna_length": 1788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"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.505A>C",
"hgvs_p": "p.Asn169His",
"transcript": "ENST00000396913.6",
"protein_id": "ENSP00000380121.2",
"transcript_support_level": 5,
"aa_start": 169,
"aa_end": null,
"aa_length": 238,
"cds_start": 505,
"cds_end": null,
"cds_length": 717,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 1732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"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.505A>C",
"hgvs_p": "p.Asn169His",
"transcript": "ENST00000453759.6",
"protein_id": "ENSP00000412525.2",
"transcript_support_level": 5,
"aa_start": 169,
"aa_end": null,
"aa_length": 175,
"cds_start": 505,
"cds_end": null,
"cds_length": 528,
"cdna_start": 860,
"cdna_end": null,
"cdna_length": 883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"dbsnp": "rs104894179",
"frequency_reference_population": 0.0000027361878,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273619,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9838299751281738,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.893,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9268,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.3,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.982,
"phylop100way_prediction": "Pathogenic",
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000263038.9",
"gene_symbol": "PHYH",
"hgnc_id": 8940,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.805A>C",
"hgvs_p": "p.Asn269His"
}
],
"clinvar_disease": " 1, ADULT,REFSUM DISEASE",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "REFSUM DISEASE, ADULT, 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}