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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: 5-132312237-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=132312237&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 132312237,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000200652.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A4",
"gene_hgnc_id": 10968,
"hgvs_c": "c.470C>A",
"hgvs_p": "p.Ser157Tyr",
"transcript": "NM_003059.3",
"protein_id": "NP_003050.2",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 551,
"cds_start": 470,
"cds_end": null,
"cds_length": 1656,
"cdna_start": 693,
"cdna_end": null,
"cdna_length": 2234,
"mane_select": "ENST00000200652.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A4",
"gene_hgnc_id": 10968,
"hgvs_c": "c.470C>A",
"hgvs_p": "p.Ser157Tyr",
"transcript": "ENST00000200652.4",
"protein_id": "ENSP00000200652.3",
"transcript_support_level": 1,
"aa_start": 157,
"aa_end": null,
"aa_length": 551,
"cds_start": 470,
"cds_end": null,
"cds_length": 1656,
"cdna_start": 693,
"cdna_end": null,
"cdna_length": 2234,
"mane_select": "NM_003059.3",
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR3936HG",
"gene_hgnc_id": 40538,
"hgvs_c": "n.841G>T",
"hgvs_p": null,
"transcript": "ENST00000621103.4",
"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": 1793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A4",
"gene_hgnc_id": 10968,
"hgvs_c": "c.470C>A",
"hgvs_p": "p.Ser157Tyr",
"transcript": "XM_047417594.1",
"protein_id": "XP_047273550.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 491,
"cds_start": 470,
"cds_end": null,
"cds_length": 1476,
"cdna_start": 693,
"cdna_end": null,
"cdna_length": 1788,
"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": "SLC22A4",
"gene_hgnc_id": 10968,
"hgvs_c": "n.274C>A",
"hgvs_p": null,
"transcript": "ENST00000491257.1",
"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": 564,
"mane_select": null,
"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": "MIR3936HG",
"gene_hgnc_id": 40538,
"hgvs_c": "n.467G>T",
"hgvs_p": null,
"transcript": "ENST00000669845.1",
"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": 1181,
"mane_select": null,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR3936HG",
"gene_hgnc_id": 40538,
"hgvs_c": "n.841G>T",
"hgvs_p": null,
"transcript": "NR_110997.1",
"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": 1802,
"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": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A4",
"gene_hgnc_id": 10968,
"hgvs_c": "c.-59C>A",
"hgvs_p": null,
"transcript": "XM_017009776.2",
"protein_id": "XP_016865265.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 375,
"cds_start": -4,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1821,
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC22A4",
"gene_hgnc_id": 10968,
"hgvs_c": "c.394-1377C>A",
"hgvs_p": null,
"transcript": "XM_011543589.3",
"protein_id": "XP_011541891.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 459,
"cds_start": -4,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1958,
"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": "SLC22A4",
"gene_hgnc_id": 10968,
"hgvs_c": "c.-31-1377C>A",
"hgvs_p": null,
"transcript": "XM_006714675.5",
"protein_id": "XP_006714738.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 375,
"cds_start": -4,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC22A4",
"gene_hgnc_id": 10968,
"dbsnp": "rs781338157",
"frequency_reference_population": 0.000001368768,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136877,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9348552227020264,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.843,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8801,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.26,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000200652.4",
"gene_symbol": "SLC22A4",
"hgnc_id": 10968,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.470C>A",
"hgvs_p": "p.Ser157Tyr"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000621103.4",
"gene_symbol": "MIR3936HG",
"hgnc_id": 40538,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.841G>T",
"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
}