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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: 19-32862482-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=32862482&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 32862482,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000023064.9",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "NM_014270.5",
"protein_id": "NP_055085.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 487,
"cds_start": 583,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 1766,
"mane_select": "ENST00000023064.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "ENST00000023064.9",
"protein_id": "ENSP00000023064.3",
"transcript_support_level": 1,
"aa_start": 195,
"aa_end": null,
"aa_length": 487,
"cds_start": 583,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 1766,
"mane_select": "NM_014270.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "ENST00000587772.1",
"protein_id": "ENSP00000468439.1",
"transcript_support_level": 1,
"aa_start": 195,
"aa_end": null,
"aa_length": 487,
"cds_start": 583,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 1568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "ENST00000590341.5",
"protein_id": "ENSP00000464822.1",
"transcript_support_level": 1,
"aa_start": 195,
"aa_end": null,
"aa_length": 487,
"cds_start": 583,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 760,
"cdna_end": null,
"cdna_length": 1752,
"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": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "n.*210+1614G>A",
"hgvs_p": null,
"transcript": "ENST00000592232.5",
"protein_id": "ENSP00000465563.1",
"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": 1030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "NM_001126335.2",
"protein_id": "NP_001119807.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 487,
"cds_start": 583,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 690,
"cdna_end": null,
"cdna_length": 1680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "NM_001243036.2",
"protein_id": "NP_001229965.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 487,
"cds_start": 583,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 785,
"cdna_end": null,
"cdna_length": 1775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "XM_011526402.4",
"protein_id": "XP_011524704.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 487,
"cds_start": 583,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 699,
"cdna_end": null,
"cdna_length": 1689,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "c.319G>A",
"hgvs_p": "p.Gly107Arg",
"transcript": "XM_017026230.1",
"protein_id": "XP_016881719.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 399,
"cds_start": 319,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 436,
"cdna_end": null,
"cdna_length": 1426,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "n.528G>A",
"hgvs_p": null,
"transcript": "ENST00000589659.1",
"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": 886,
"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": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "n.*210+1614G>A",
"hgvs_p": null,
"transcript": "ENST00000590465.5",
"protein_id": "ENSP00000468076.1",
"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": 1998,
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"hgvs_c": "c.23+1614G>A",
"hgvs_p": null,
"transcript": "XM_047438117.1",
"protein_id": "XP_047294073.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 260,
"cds_start": -4,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC7A9",
"gene_hgnc_id": 11067,
"dbsnp": "rs121908482",
"frequency_reference_population": 0.000009582714,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000958271,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9959650635719299,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.959,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9902,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.47,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.874,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.06,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM1",
"PM5",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000023064.9",
"gene_symbol": "SLC7A9",
"hgnc_id": 11067,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg"
}
],
"clinvar_disease": "Cystinuria",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Cystinuria",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}