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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: 3-171007166-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=171007166&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 171007166,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000314251.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.594G>A",
"hgvs_p": "p.Thr198Thr",
"transcript": "NM_000340.2",
"protein_id": "NP_000331.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 524,
"cds_start": 594,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 644,
"cdna_end": null,
"cdna_length": 3181,
"mane_select": "ENST00000314251.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.594G>A",
"hgvs_p": "p.Thr198Thr",
"transcript": "ENST00000314251.8",
"protein_id": "ENSP00000323568.3",
"transcript_support_level": 1,
"aa_start": 198,
"aa_end": null,
"aa_length": 524,
"cds_start": 594,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 644,
"cdna_end": null,
"cdna_length": 3181,
"mane_select": "NM_000340.2",
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "n.*61G>A",
"hgvs_p": null,
"transcript": "ENST00000497642.5",
"protein_id": "ENSP00000418456.1",
"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": 2583,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "n.*61G>A",
"hgvs_p": null,
"transcript": "ENST00000497642.5",
"protein_id": "ENSP00000418456.1",
"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": 2583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.237G>A",
"hgvs_p": "p.Thr79Thr",
"transcript": "NM_001278658.2",
"protein_id": "NP_001265587.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 405,
"cds_start": 237,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 2918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Thr25Thr",
"transcript": "NM_001278659.2",
"protein_id": "NP_001265588.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 351,
"cds_start": 75,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 519,
"cdna_end": null,
"cdna_length": 3056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Thr25Thr",
"transcript": "ENST00000461867.1",
"protein_id": "ENSP00000418888.1",
"transcript_support_level": 3,
"aa_start": 25,
"aa_end": null,
"aa_length": 102,
"cds_start": 75,
"cds_end": null,
"cds_length": 309,
"cdna_start": 191,
"cdna_end": null,
"cdna_length": 425,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.549G>A",
"hgvs_p": "p.Thr183Thr",
"transcript": "XM_011513087.3",
"protein_id": "XP_011511389.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 509,
"cds_start": 549,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 628,
"cdna_end": null,
"cdna_length": 3165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.75G>A",
"hgvs_p": "p.Thr25Thr",
"transcript": "XM_047448761.1",
"protein_id": "XP_047304717.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 351,
"cds_start": 75,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 167,
"cdna_end": null,
"cdna_length": 2704,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "n.*61G>A",
"hgvs_p": null,
"transcript": "ENST00000469787.1",
"protein_id": "ENSP00000417918.1",
"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": 1533,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "n.305G>A",
"hgvs_p": null,
"transcript": "ENST00000471379.1",
"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": 380,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "n.*61G>A",
"hgvs_p": null,
"transcript": "ENST00000469787.1",
"protein_id": "ENSP00000417918.1",
"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": 1533,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.291+12141C>T",
"hgvs_p": null,
"transcript": "ENST00000655926.1",
"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": 453,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.309+12141C>T",
"hgvs_p": null,
"transcript": "ENST00000834079.1",
"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": 1483,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.476+12141C>T",
"hgvs_p": null,
"transcript": "ENST00000834080.1",
"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": 692,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.486+12141C>T",
"hgvs_p": null,
"transcript": "ENST00000834081.1",
"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": 1037,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.484+12141C>T",
"hgvs_p": null,
"transcript": "ENST00000834082.1",
"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": 1656,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.448+12141C>T",
"hgvs_p": null,
"transcript": "ENST00000834083.1",
"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": 610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"dbsnp": "rs5404",
"frequency_reference_population": 0.10754832,
"hom_count_reference_population": 11275,
"allele_count_reference_population": 173036,
"gnomad_exomes_af": 0.102868,
"gnomad_genomes_af": 0.152455,
"gnomad_exomes_ac": 149886,
"gnomad_genomes_ac": 23150,
"gnomad_exomes_homalt": 8873,
"gnomad_genomes_homalt": 2402,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7200000286102295,
"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": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.139,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000314251.8",
"gene_symbol": "SLC2A2",
"hgnc_id": 11006,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.594G>A",
"hgvs_p": "p.Thr198Thr"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000655926.1",
"gene_symbol": "ENSG00000286856",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.291+12141C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Fanconi-Bickel syndrome,Type 2 diabetes mellitus,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Fanconi-Bickel syndrome|Type 2 diabetes mellitus|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}