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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: 3-12161366-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=12161366&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 12161366,
"ref": "C",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000621198.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "c.775-180C>A",
"hgvs_p": null,
"transcript": "NM_133625.6",
"protein_id": "NP_598328.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 582,
"cds_start": -4,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3320,
"mane_select": "ENST00000621198.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "c.775-180C>A",
"hgvs_p": null,
"transcript": "ENST00000621198.5",
"protein_id": "ENSP00000480050.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 582,
"cds_start": -4,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3320,
"mane_select": "NM_133625.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "c.775-180C>A",
"hgvs_p": null,
"transcript": "ENST00000620175.4",
"protein_id": "ENSP00000484916.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 478,
"cds_start": -4,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "c.775-180C>A",
"hgvs_p": null,
"transcript": "NM_003178.6",
"protein_id": "NP_003169.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 478,
"cds_start": -4,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3888,
"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": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "n.226-180C>A",
"hgvs_p": null,
"transcript": "ENST00000439861.5",
"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": 2128,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "n.224-180C>A",
"hgvs_p": null,
"transcript": "ENST00000447752.2",
"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": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "c.775-180C>A",
"hgvs_p": null,
"transcript": "XM_006713311.4",
"protein_id": "XP_006713374.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 511,
"cds_start": -4,
"cds_end": null,
"cds_length": 1536,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3115,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "c.292-180C>A",
"hgvs_p": null,
"transcript": "XM_006713312.5",
"protein_id": "XP_006713375.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 421,
"cds_start": -4,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "c.103-180C>A",
"hgvs_p": null,
"transcript": "XM_017007087.2",
"protein_id": "XP_016862576.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 358,
"cds_start": -4,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3082,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "c.4-180C>A",
"hgvs_p": null,
"transcript": "XM_006713313.3",
"protein_id": "XP_006713376.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 325,
"cds_start": -4,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2688,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"hgvs_c": "n.-180C>A",
"hgvs_p": null,
"transcript": "ENST00000425297.2",
"protein_id": "ENSP00000480038.1",
"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": 2356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SYN2",
"gene_hgnc_id": 11495,
"dbsnp": "rs308950",
"frequency_reference_population": 0.000013151492,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131515,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9100000262260437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.91,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.067,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000621198.5",
"gene_symbol": "SYN2",
"hgnc_id": 11495,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.775-180C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}