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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: 10-13283750-AAC-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=13283750&ref=AAC&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 13283750,
"ref": "AAC",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000263038.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.766_767delGT",
"hgvs_p": "p.Val256fs",
"transcript": "NM_006214.4",
"protein_id": "NP_006205.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 338,
"cds_start": 766,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 789,
"cdna_end": null,
"cdna_length": 1541,
"mane_select": "ENST00000263038.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.766_767delGT",
"hgvs_p": "p.Val256fs",
"transcript": "ENST00000263038.9",
"protein_id": "ENSP00000263038.4",
"transcript_support_level": 1,
"aa_start": 256,
"aa_end": null,
"aa_length": 338,
"cds_start": 766,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 789,
"cdna_end": null,
"cdna_length": 1541,
"mane_select": "NM_006214.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.772_773delGT",
"hgvs_p": "p.Val258fs",
"transcript": "NM_001323082.2",
"protein_id": "NP_001310011.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 340,
"cds_start": 772,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 1547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.715_716delGT",
"hgvs_p": "p.Val239fs",
"transcript": "ENST00000396920.7",
"protein_id": "ENSP00000380126.3",
"transcript_support_level": 5,
"aa_start": 239,
"aa_end": null,
"aa_length": 321,
"cds_start": 715,
"cds_end": null,
"cds_length": 966,
"cdna_start": 1121,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.502_503delGT",
"hgvs_p": "p.Val168fs",
"transcript": "NM_001323083.2",
"protein_id": "NP_001310012.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 250,
"cds_start": 502,
"cds_end": null,
"cds_length": 753,
"cdna_start": 525,
"cdna_end": null,
"cdna_length": 1277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.472_473delGT",
"hgvs_p": "p.Val158fs",
"transcript": "NM_001323084.2",
"protein_id": "NP_001310013.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 240,
"cds_start": 472,
"cds_end": null,
"cds_length": 723,
"cdna_start": 983,
"cdna_end": null,
"cdna_length": 1735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.466_467delGT",
"hgvs_p": "p.Val156fs",
"transcript": "NM_001037537.2",
"protein_id": "NP_001032626.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 238,
"cds_start": 466,
"cds_end": null,
"cds_length": 717,
"cdna_start": 977,
"cdna_end": null,
"cdna_length": 1729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.466_467delGT",
"hgvs_p": "p.Val156fs",
"transcript": "NM_001323080.2",
"protein_id": "NP_001310009.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 238,
"cds_start": 466,
"cds_end": null,
"cds_length": 717,
"cdna_start": 1036,
"cdna_end": null,
"cdna_length": 1788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.466_467delGT",
"hgvs_p": "p.Val156fs",
"transcript": "ENST00000396913.6",
"protein_id": "ENSP00000380121.2",
"transcript_support_level": 5,
"aa_start": 156,
"aa_end": null,
"aa_length": 238,
"cds_start": 466,
"cds_end": null,
"cds_length": 717,
"cdna_start": 977,
"cdna_end": null,
"cdna_length": 1732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_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.466_467delGT",
"hgvs_p": "p.Val156fs",
"transcript": "ENST00000453759.6",
"protein_id": "ENSP00000412525.2",
"transcript_support_level": 5,
"aa_start": 156,
"aa_end": null,
"aa_length": 175,
"cds_start": 466,
"cds_end": null,
"cds_length": 528,
"cdna_start": 822,
"cdna_end": null,
"cdna_length": 883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHYH",
"gene_hgnc_id": 8940,
"dbsnp": "rs797045100",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.214,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000263038.9",
"gene_symbol": "PHYH",
"hgnc_id": 8940,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.766_767delGT",
"hgvs_p": "p.Val256fs"
}
],
"clinvar_disease": "Phytanic acid storage disease",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Phytanic acid storage disease",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}