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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: 17-28405231-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=28405231&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 28405231,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_080669.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.466G>T",
"hgvs_p": "p.Asp156Tyr",
"transcript": "NM_080669.6",
"protein_id": "NP_542400.2",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 459,
"cds_start": 466,
"cds_end": null,
"cds_length": 1380,
"cdna_start": 564,
"cdna_end": null,
"cdna_length": 6492,
"mane_select": "ENST00000612814.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.466G>T",
"hgvs_p": "p.Asp156Tyr",
"transcript": "ENST00000612814.5",
"protein_id": "ENSP00000480703.1",
"transcript_support_level": 2,
"aa_start": 156,
"aa_end": null,
"aa_length": 459,
"cds_start": 466,
"cds_end": null,
"cds_length": 1380,
"cdna_start": 564,
"cdna_end": null,
"cdna_length": 6492,
"mane_select": "NM_080669.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.466G>T",
"hgvs_p": "p.Asp156Tyr",
"transcript": "ENST00000618626.1",
"protein_id": "ENSP00000483652.1",
"transcript_support_level": 1,
"aa_start": 156,
"aa_end": null,
"aa_length": 431,
"cds_start": 466,
"cds_end": null,
"cds_length": 1296,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 5363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.466G>T",
"hgvs_p": "p.Asp156Tyr",
"transcript": "NM_001242366.3",
"protein_id": "NP_001229295.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 431,
"cds_start": 466,
"cds_end": null,
"cds_length": 1296,
"cdna_start": 564,
"cdna_end": null,
"cdna_length": 6408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.244G>T",
"hgvs_p": "p.Asp82Tyr",
"transcript": "ENST00000584995.5",
"protein_id": "ENSP00000464190.1",
"transcript_support_level": 3,
"aa_start": 82,
"aa_end": null,
"aa_length": 249,
"cds_start": 244,
"cds_end": null,
"cds_length": 751,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 1030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.202G>T",
"hgvs_p": "p.Asp68Tyr",
"transcript": "ENST00000584426.1",
"protein_id": "ENSP00000467416.1",
"transcript_support_level": 4,
"aa_start": 68,
"aa_end": null,
"aa_length": 127,
"cds_start": 202,
"cds_end": null,
"cds_length": 385,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 564,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.466G>T",
"hgvs_p": "p.Asp156Tyr",
"transcript": "XM_005277786.4",
"protein_id": "XP_005277843.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 415,
"cds_start": 466,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 564,
"cdna_end": null,
"cdna_length": 6251,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.244G>T",
"hgvs_p": "p.Asp82Tyr",
"transcript": "XM_017024110.2",
"protein_id": "XP_016879599.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 385,
"cds_start": 244,
"cds_end": null,
"cds_length": 1158,
"cdna_start": 485,
"cdna_end": null,
"cdna_length": 6413,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.244G>T",
"hgvs_p": "p.Asp82Tyr",
"transcript": "XM_047435279.1",
"protein_id": "XP_047291235.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 357,
"cds_start": 244,
"cds_end": null,
"cds_length": 1074,
"cdna_start": 485,
"cdna_end": null,
"cdna_length": 6329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.244G>T",
"hgvs_p": "p.Asp82Tyr",
"transcript": "XM_047435280.1",
"protein_id": "XP_047291236.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 341,
"cds_start": 244,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 485,
"cdna_end": null,
"cdna_length": 6172,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000265254",
"gene_hgnc_id": null,
"hgvs_c": "n.236C>A",
"hgvs_p": null,
"transcript": "ENST00000580714.2",
"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": 1113,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "n.520G>T",
"hgvs_p": null,
"transcript": "ENST00000582590.1",
"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": 1435,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "n.67+450G>T",
"hgvs_p": null,
"transcript": "ENST00000578217.1",
"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": 596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"hgvs_c": "c.*146G>T",
"hgvs_p": null,
"transcript": "ENST00000581516.1",
"protein_id": "ENSP00000462942.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 31,
"cds_start": -4,
"cds_end": null,
"cds_length": 98,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC46A1",
"gene_hgnc_id": 30521,
"dbsnp": "rs281875210",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9214437007904053,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.867,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7827,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.495,
"phylop100way_prediction": "Uncertain_significance",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_080669.6",
"gene_symbol": "SLC46A1",
"hgnc_id": 30521,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.466G>T",
"hgvs_p": "p.Asp156Tyr"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000580714.2",
"gene_symbol": "ENSG00000265254",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.236C>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "not provided",
"clinvar_review_status": "no classification provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "not provided",
"custom_annotations": null
}
],
"message": null
}