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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: 22-35400477-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=35400477&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 35400477,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_006739.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asp13Asp",
"transcript": "NM_006739.4",
"protein_id": "NP_006730.2",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 734,
"cds_start": 39,
"cds_end": null,
"cds_length": 2205,
"cdna_start": 116,
"cdna_end": null,
"cdna_length": 3458,
"mane_select": "ENST00000216122.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asp13Asp",
"transcript": "ENST00000216122.9",
"protein_id": "ENSP00000216122.3",
"transcript_support_level": 1,
"aa_start": 13,
"aa_end": null,
"aa_length": 734,
"cds_start": 39,
"cds_end": null,
"cds_length": 2205,
"cdna_start": 116,
"cdna_end": null,
"cdna_length": 3458,
"mane_select": "NM_006739.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asp13Asp",
"transcript": "ENST00000382011.9",
"protein_id": "ENSP00000371441.5",
"transcript_support_level": 2,
"aa_start": 13,
"aa_end": null,
"aa_length": 691,
"cds_start": 39,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 119,
"cdna_end": null,
"cdna_length": 2402,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asp13Asp",
"transcript": "ENST00000416905.1",
"protein_id": "ENSP00000393977.1",
"transcript_support_level": 3,
"aa_start": 13,
"aa_end": null,
"aa_length": 229,
"cds_start": 39,
"cds_end": null,
"cds_length": 692,
"cdna_start": 86,
"cdna_end": null,
"cdna_length": 739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asp13Asp",
"transcript": "XM_006724242.5",
"protein_id": "XP_006724305.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 732,
"cds_start": 39,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 116,
"cdna_end": null,
"cdna_length": 2908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asp13Asp",
"transcript": "XM_047441366.1",
"protein_id": "XP_047297322.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 732,
"cds_start": 39,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 116,
"cdna_end": null,
"cdna_length": 2911,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"hgvs_c": "n.39C>T",
"hgvs_p": null,
"transcript": "ENST00000451351.5",
"protein_id": "ENSP00000412847.1",
"transcript_support_level": 4,
"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": 450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"hgvs_c": "c.-53C>T",
"hgvs_p": null,
"transcript": "ENST00000444778.1",
"protein_id": "ENSP00000408705.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 149,
"cds_start": -4,
"cds_end": null,
"cds_length": 452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"hgvs_c": "n.26+310C>T",
"hgvs_p": null,
"transcript": "ENST00000417343.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MCM5",
"gene_hgnc_id": 6948,
"dbsnp": null,
"frequency_reference_population": 0.0000020523262,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205233,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.38999998569488525,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.723,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_006739.4",
"gene_symbol": "MCM5",
"hgnc_id": 6948,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asp13Asp"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}