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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: 3-86990639-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=86990639&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 86990639,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000398399.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VGLL3",
"gene_hgnc_id": 24327,
"hgvs_c": "c.105G>A",
"hgvs_p": "p.Pro35Pro",
"transcript": "NM_016206.4",
"protein_id": "NP_057290.2",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 326,
"cds_start": 105,
"cds_end": null,
"cds_length": 981,
"cdna_start": 511,
"cdna_end": null,
"cdna_length": 10438,
"mane_select": "ENST00000398399.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VGLL3",
"gene_hgnc_id": 24327,
"hgvs_c": "c.105G>A",
"hgvs_p": "p.Pro35Pro",
"transcript": "ENST00000398399.7",
"protein_id": "ENSP00000381436.2",
"transcript_support_level": 1,
"aa_start": 35,
"aa_end": null,
"aa_length": 326,
"cds_start": 105,
"cds_end": null,
"cds_length": 981,
"cdna_start": 511,
"cdna_end": null,
"cdna_length": 10438,
"mane_select": "NM_016206.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VGLL3",
"gene_hgnc_id": 24327,
"hgvs_c": "c.105G>A",
"hgvs_p": "p.Pro35Pro",
"transcript": "ENST00000383698.3",
"protein_id": "ENSP00000373199.3",
"transcript_support_level": 1,
"aa_start": 35,
"aa_end": null,
"aa_length": 320,
"cds_start": 105,
"cds_end": null,
"cds_length": 963,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 2475,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VGLL3",
"gene_hgnc_id": 24327,
"hgvs_c": "c.105G>A",
"hgvs_p": "p.Pro35Pro",
"transcript": "NM_001320493.2",
"protein_id": "NP_001307422.1",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 320,
"cds_start": 105,
"cds_end": null,
"cds_length": 963,
"cdna_start": 511,
"cdna_end": null,
"cdna_length": 2505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VGLL3",
"gene_hgnc_id": 24327,
"hgvs_c": "c.105G>A",
"hgvs_p": "p.Pro35Pro",
"transcript": "NM_001320494.2",
"protein_id": "NP_001307423.1",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 273,
"cds_start": 105,
"cds_end": null,
"cds_length": 822,
"cdna_start": 511,
"cdna_end": null,
"cdna_length": 10279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VGLL3",
"gene_hgnc_id": 24327,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Pro21Pro",
"transcript": "ENST00000494229.1",
"protein_id": "ENSP00000419115.1",
"transcript_support_level": 3,
"aa_start": 21,
"aa_end": null,
"aa_length": 206,
"cds_start": 63,
"cds_end": null,
"cds_length": 623,
"cdna_start": 64,
"cdna_end": null,
"cdna_length": 624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VGLL3",
"gene_hgnc_id": 24327,
"hgvs_c": "c.105G>A",
"hgvs_p": "p.Pro35Pro",
"transcript": "XM_006713138.5",
"protein_id": "XP_006713201.1",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 325,
"cds_start": 105,
"cds_end": null,
"cds_length": 978,
"cdna_start": 511,
"cdna_end": null,
"cdna_length": 10435,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VGLL3",
"gene_hgnc_id": 24327,
"dbsnp": null,
"frequency_reference_population": 0.0000032819328,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000328193,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03200000151991844,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.032,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.364,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000398399.7",
"gene_symbol": "VGLL3",
"hgnc_id": 24327,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.105G>A",
"hgvs_p": "p.Pro35Pro"
}
],
"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
}