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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: 2-227685582-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227685582&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 227685582,
"ref": "T",
"alt": "G",
"effect": "3_prime_UTR_variant",
"transcript": "NM_025243.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.*1815A>C",
"hgvs_p": null,
"transcript": "NM_025243.4",
"protein_id": "NP_079519.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 496,
"cds_start": -4,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5213,
"mane_select": "ENST00000644224.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.*1815A>C",
"hgvs_p": null,
"transcript": "ENST00000644224.2",
"protein_id": "ENSP00000495385.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 496,
"cds_start": -4,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5213,
"mane_select": "NM_025243.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "n.*2294A>C",
"hgvs_p": null,
"transcript": "ENST00000647113.1",
"protein_id": "ENSP00000494966.1",
"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": 2851,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.*1815A>C",
"hgvs_p": null,
"transcript": "NM_001371411.1",
"protein_id": "NP_001358340.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 496,
"cds_start": -4,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5303,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.*1815A>C",
"hgvs_p": null,
"transcript": "NM_001371412.1",
"protein_id": "NP_001358341.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 496,
"cds_start": -4,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5469,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.*1815A>C",
"hgvs_p": null,
"transcript": "NM_001371413.1",
"protein_id": "NP_001358342.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 492,
"cds_start": -4,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5409,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.*1815A>C",
"hgvs_p": null,
"transcript": "NM_001371414.1",
"protein_id": "NP_001358343.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 492,
"cds_start": -4,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"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": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "n.*2294A>C",
"hgvs_p": null,
"transcript": "ENST00000647113.1",
"protein_id": "ENSP00000494966.1",
"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": 2851,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.*1815A>C",
"hgvs_p": null,
"transcript": "XM_047445927.1",
"protein_id": "XP_047301883.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 508,
"cds_start": -4,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5642,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "n.*98A>C",
"hgvs_p": null,
"transcript": "ENST00000676066.1",
"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": 2938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"dbsnp": "rs34020562",
"frequency_reference_population": 0.3765709,
"hom_count_reference_population": 11628,
"allele_count_reference_population": 57232,
"gnomad_exomes_af": 0.125,
"gnomad_genomes_af": 0.376584,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 57231,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 11628,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8899999856948853,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.214,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_025243.4",
"gene_symbol": "SLC19A3",
"hgnc_id": 16266,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*1815A>C",
"hgvs_p": null
}
],
"clinvar_disease": "Biotin-responsive basal ganglia disease,Thiamine Metabolism Dysfunction Syndrome,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Thiamine Metabolism Dysfunction Syndrome|Biotin-responsive basal ganglia disease|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}