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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: 22-18083522-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=18083522&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 18083522,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_017929.6",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.457C>G",
"hgvs_p": "p.Leu153Val",
"transcript": "NM_001127649.3",
"protein_id": "NP_001121121.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 305,
"cds_start": 457,
"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": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.457C>G",
"hgvs_p": "p.Leu153Val",
"transcript": "ENST00000399744.8",
"protein_id": "ENSP00000382648.4",
"transcript_support_level": 1,
"aa_start": 153,
"aa_end": null,
"aa_length": 305,
"cds_start": 457,
"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": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.457C>G",
"hgvs_p": "p.Leu153Val",
"transcript": "ENST00000329627.11",
"protein_id": "ENSP00000331106.5",
"transcript_support_level": 1,
"aa_start": 153,
"aa_end": null,
"aa_length": 305,
"cds_start": 457,
"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": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.457C>G",
"hgvs_p": "p.Leu153Val",
"transcript": "ENST00000428061.2",
"protein_id": "ENSP00000412441.2",
"transcript_support_level": 1,
"aa_start": 153,
"aa_end": null,
"aa_length": 256,
"cds_start": 457,
"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": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288683",
"gene_hgnc_id": null,
"hgvs_c": "n.457C>G",
"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": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.532C>G",
"hgvs_p": "p.Leu178Val",
"transcript": "ENST00000936123.1",
"protein_id": "ENSP00000606182.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 330,
"cds_start": 532,
"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": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.457C>G",
"hgvs_p": "p.Leu153Val",
"transcript": "NM_017929.6",
"protein_id": "NP_060399.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 305,
"cds_start": 457,
"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": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.457C>G",
"hgvs_p": "p.Leu153Val",
"transcript": "ENST00000851847.1",
"protein_id": "ENSP00000521906.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 262,
"cds_start": 457,
"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": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"hgvs_c": "c.457C>G",
"hgvs_p": "p.Leu153Val",
"transcript": "NM_001199319.2",
"protein_id": "NP_001186248.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 256,
"cds_start": 457,
"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"
}
],
"gene_symbol": "PEX26",
"gene_hgnc_id": 22965,
"dbsnp": "rs12484657",
"frequency_reference_population": 0.015182735,
"hom_count_reference_population": 232,
"allele_count_reference_population": 24507,
"gnomad_exomes_af": 0.0156637,
"gnomad_genomes_af": 0.0105679,
"gnomad_exomes_ac": 22897,
"gnomad_genomes_ac": 1610,
"gnomad_exomes_homalt": 211,
"gnomad_genomes_homalt": 21,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00920453667640686,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.513,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1207,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.217,
"phylop100way_prediction": "Benign",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_017929.6",
"gene_symbol": "PEX26",
"hgnc_id": 22965,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.457C>G",
"hgvs_p": "p.Leu153Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000474897.6",
"gene_symbol": "ENSG00000288683",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.457C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Peroxisome biogenesis disorder 1A (Zellweger),Peroxisome biogenesis disorder 7A (Zellweger),Peroxisome biogenesis disorder 7B,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:7",
"phenotype_combined": "not specified|not provided|Peroxisome biogenesis disorder 1A (Zellweger)|Peroxisome biogenesis disorder 7A (Zellweger);Peroxisome biogenesis disorder 7B|Peroxisome biogenesis disorder 7A (Zellweger)",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}