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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: 22-18078403-AG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=18078403&ref=AG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 18078403,
"ref": "AG",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "NM_017929.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.28delG",
"hgvs_p": "p.Ala10fs",
"transcript": "NM_001127649.3",
"protein_id": "NP_001121121.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 305,
"cds_start": 28,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000399744.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001127649.3"
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.28delG",
"hgvs_p": "p.Ala10fs",
"transcript": "ENST00000399744.8",
"protein_id": "ENSP00000382648.4",
"transcript_support_level": 1,
"aa_start": 10,
"aa_end": null,
"aa_length": 305,
"cds_start": 28,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001127649.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000399744.8"
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.28delG",
"hgvs_p": "p.Ala10fs",
"transcript": "ENST00000329627.11",
"protein_id": "ENSP00000331106.5",
"transcript_support_level": 1,
"aa_start": 10,
"aa_end": null,
"aa_length": 305,
"cds_start": 28,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000329627.11"
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.28delG",
"hgvs_p": "p.Ala10fs",
"transcript": "ENST00000428061.2",
"protein_id": "ENSP00000412441.2",
"transcript_support_level": 1,
"aa_start": 10,
"aa_end": null,
"aa_length": 256,
"cds_start": 28,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428061.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288683",
"gene_hgnc_id": null,
"hgvs_c": "n.28delG",
"hgvs_p": null,
"transcript": "ENST00000474897.6",
"protein_id": "ENSP00000434235.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000474897.6"
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.28delG",
"hgvs_p": "p.Ala10fs",
"transcript": "ENST00000936123.1",
"protein_id": "ENSP00000606182.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 330,
"cds_start": 28,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936123.1"
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.28delG",
"hgvs_p": "p.Ala10fs",
"transcript": "NM_017929.6",
"protein_id": "NP_060399.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 305,
"cds_start": 28,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017929.6"
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.28delG",
"hgvs_p": "p.Ala10fs",
"transcript": "ENST00000851847.1",
"protein_id": "ENSP00000521906.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 262,
"cds_start": 28,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851847.1"
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.28delG",
"hgvs_p": "p.Ala10fs",
"transcript": "NM_001199319.2",
"protein_id": "NP_001186248.1",
"transcript_support_level": null,
"aa_start": 10,
"aa_end": null,
"aa_length": 256,
"cds_start": 28,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199319.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000225335",
"gene_hgnc_id": null,
"hgvs_c": "n.481delC",
"hgvs_p": null,
"transcript": "ENST00000607927.2",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000607927.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000225335",
"gene_hgnc_id": null,
"hgvs_c": "n.372delC",
"hgvs_p": null,
"transcript": "ENST00000622035.1",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000622035.1"
}
],
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"dbsnp": "rs1926386296",
"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": 0.25,
"splice_prediction_selected": "Uncertain_significance",
"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": 4.568,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.25,
"spliceai_max_prediction": "Uncertain_significance",
"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": "NM_017929.6",
"gene_symbol": "PEX26",
"hgnc_id": 22965,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.28delG",
"hgvs_p": "p.Ala10fs"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000474897.6",
"gene_symbol": "ENSG00000288683",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.28delG",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000607927.2",
"gene_symbol": "ENSG00000225335",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.481delC",
"hgvs_p": null
}
],
"clinvar_disease": "Peroxisome biogenesis disorder 7A (Zellweger),Peroxisome biogenesis disorder 7B",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Peroxisome biogenesis disorder 7A (Zellweger);Peroxisome biogenesis disorder 7B",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}