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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: X-153740136-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153740136&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153740136,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000218104.6",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1533C>T",
"hgvs_p": "p.Cys511Cys",
"transcript": "NM_000033.4",
"protein_id": "NP_000024.2",
"transcript_support_level": null,
"aa_start": 511,
"aa_end": null,
"aa_length": 745,
"cds_start": 1533,
"cds_end": null,
"cds_length": 2238,
"cdna_start": 1944,
"cdna_end": null,
"cdna_length": 3669,
"mane_select": "ENST00000218104.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1533C>T",
"hgvs_p": "p.Cys511Cys",
"transcript": "ENST00000218104.6",
"protein_id": "ENSP00000218104.3",
"transcript_support_level": 1,
"aa_start": 511,
"aa_end": null,
"aa_length": 745,
"cds_start": 1533,
"cds_end": null,
"cds_length": 2238,
"cdna_start": 1944,
"cdna_end": null,
"cdna_length": 3669,
"mane_select": "NM_000033.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1589C>T",
"hgvs_p": "p.Ala530Val",
"transcript": "XM_047441917.1",
"protein_id": "XP_047297873.1",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 575,
"cds_start": 1589,
"cds_end": null,
"cds_length": 1728,
"cdna_start": 2000,
"cdna_end": null,
"cdna_length": 2238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1833C>T",
"hgvs_p": "p.Cys611Cys",
"transcript": "NM_001440747.1",
"protein_id": "NP_001427676.1",
"transcript_support_level": null,
"aa_start": 611,
"aa_end": null,
"aa_length": 845,
"cds_start": 1833,
"cds_end": null,
"cds_length": 2538,
"cdna_start": 2244,
"cdna_end": null,
"cdna_length": 3969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "n.536C>T",
"hgvs_p": null,
"transcript": "ENST00000443684.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.72-1558G>A",
"hgvs_p": null,
"transcript": "ENST00000434284.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.90-1558G>A",
"hgvs_p": null,
"transcript": "NR_199693.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.198-1558G>A",
"hgvs_p": null,
"transcript": "NR_199694.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.309-1558G>A",
"hgvs_p": null,
"transcript": "NR_199695.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.230-1558G>A",
"hgvs_p": null,
"transcript": "NR_199696.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3956,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"dbsnp": "rs782370364",
"frequency_reference_population": 0.000023154082,
"hom_count_reference_population": 5,
"allele_count_reference_population": 28,
"gnomad_exomes_af": 0.0000218902,
"gnomad_genomes_af": 0.0000354271,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.41600000858306885,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.416,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.096,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000218104.6",
"gene_symbol": "ABCD1",
"hgnc_id": 61,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.1533C>T",
"hgvs_p": "p.Cys511Cys"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000434284.1",
"gene_symbol": "PLXNB3-AS1",
"hgnc_id": 40454,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.72-1558G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Adrenoleukodystrophy",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Adrenoleukodystrophy",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}