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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: 12-6464474-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=6464474&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 6464474,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_014231.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Thr118Ile",
"transcript": "NM_014231.5",
"protein_id": "NP_055046.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 118,
"cds_start": 353,
"cds_end": null,
"cds_length": 357,
"cdna_start": 499,
"cdna_end": null,
"cdna_length": 2736,
"mane_select": "ENST00000396308.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Thr118Ile",
"transcript": "ENST00000396308.4",
"protein_id": "ENSP00000379602.3",
"transcript_support_level": 2,
"aa_start": 118,
"aa_end": null,
"aa_length": 118,
"cds_start": 353,
"cds_end": null,
"cds_length": 357,
"cdna_start": 499,
"cdna_end": null,
"cdna_length": 2736,
"mane_select": "NM_014231.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "c.*402C>T",
"hgvs_p": null,
"transcript": "ENST00000361716.8",
"protein_id": "ENSP00000355122.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 117,
"cds_start": -4,
"cds_end": null,
"cds_length": 354,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3139,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "c.340+416C>T",
"hgvs_p": null,
"transcript": "ENST00000400911.7",
"protein_id": "ENSP00000383702.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 116,
"cds_start": -4,
"cds_end": null,
"cds_length": 351,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1068,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "c.*402C>T",
"hgvs_p": null,
"transcript": "NM_199245.3",
"protein_id": "NP_954740.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 117,
"cds_start": -4,
"cds_end": null,
"cds_length": 354,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3139,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "c.340+416C>T",
"hgvs_p": null,
"transcript": "NM_001297438.2",
"protein_id": "NP_001284367.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 116,
"cds_start": -4,
"cds_end": null,
"cds_length": 351,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "c.340+416C>T",
"hgvs_p": null,
"transcript": "NM_016830.4",
"protein_id": "NP_058439.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 116,
"cds_start": -4,
"cds_end": null,
"cds_length": 351,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "c.340+416C>T",
"hgvs_p": null,
"transcript": "ENST00000535180.5",
"protein_id": "ENSP00000444181.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 116,
"cds_start": -4,
"cds_end": null,
"cds_length": 351,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 747,
"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": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "n.296+416C>T",
"hgvs_p": null,
"transcript": "ENST00000544432.5",
"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": 759,
"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": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "TAPBPL",
"gene_hgnc_id": 30683,
"hgvs_c": "n.1702-1401G>A",
"hgvs_p": null,
"transcript": "ENST00000545700.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 2344,
"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": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "n.359+416C>T",
"hgvs_p": null,
"transcript": "NR_123717.2",
"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": 965,
"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": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "TAPBPL",
"gene_hgnc_id": 30683,
"hgvs_c": "n.1708+2231G>A",
"hgvs_p": null,
"transcript": "XR_001748777.3",
"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": 3303,
"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": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "TAPBPL",
"gene_hgnc_id": 30683,
"hgvs_c": "n.1708+2231G>A",
"hgvs_p": null,
"transcript": "XR_001748778.3",
"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": 3300,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "n.*108C>T",
"hgvs_p": null,
"transcript": "ENST00000538970.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"hgvs_c": "n.*197C>T",
"hgvs_p": null,
"transcript": "ENST00000535927.5",
"protein_id": null,
"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": 578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VAMP1",
"gene_hgnc_id": 12642,
"dbsnp": "rs1232673532",
"frequency_reference_population": 0.0000032430344,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000215884,
"gnomad_genomes_af": 0.0000131465,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2666301131248474,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.317,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.438,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.665,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_014231.5",
"gene_symbol": "VAMP1",
"hgnc_id": 12642,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Thr118Ile"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000545700.5",
"gene_symbol": "TAPBPL",
"hgnc_id": 30683,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1702-1401G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Spastic paraplegia",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Spastic paraplegia",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}