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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: 3-136473546-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=136473546&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 136473546,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000383202.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"transcript": "NM_005862.3",
"protein_id": "NP_005853.2",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 1258,
"cds_start": 1118,
"cds_end": null,
"cds_length": 3777,
"cdna_start": 1385,
"cdna_end": null,
"cdna_length": 6062,
"mane_select": "ENST00000383202.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"transcript": "ENST00000383202.7",
"protein_id": "ENSP00000372689.2",
"transcript_support_level": 1,
"aa_start": 373,
"aa_end": null,
"aa_length": 1258,
"cds_start": 1118,
"cds_end": null,
"cds_length": 3777,
"cdna_start": 1385,
"cdna_end": null,
"cdna_length": 6062,
"mane_select": "NM_005862.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln",
"transcript": "ENST00000236698.9",
"protein_id": "ENSP00000236698.5",
"transcript_support_level": 1,
"aa_start": 373,
"aa_end": null,
"aa_length": 1221,
"cds_start": 1118,
"cds_end": null,
"cds_length": 3666,
"cdna_start": 1385,
"cdna_end": null,
"cdna_length": 5951,
"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": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.*1210G>A",
"hgvs_p": null,
"transcript": "ENST00000483235.5",
"protein_id": "ENSP00000419093.1",
"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": 5206,
"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": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.*757G>A",
"hgvs_p": null,
"transcript": "ENST00000487065.5",
"protein_id": "ENSP00000418472.1",
"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": 2914,
"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": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.*1210G>A",
"hgvs_p": null,
"transcript": "ENST00000483235.5",
"protein_id": "ENSP00000419093.1",
"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": 5206,
"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": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.*757G>A",
"hgvs_p": null,
"transcript": "ENST00000487065.5",
"protein_id": "ENSP00000418472.1",
"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": 2914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.440G>A",
"hgvs_p": "p.Arg147Gln",
"transcript": "ENST00000434713.6",
"protein_id": "ENSP00000404396.2",
"transcript_support_level": 5,
"aa_start": 147,
"aa_end": null,
"aa_length": 998,
"cds_start": 440,
"cds_end": null,
"cds_length": 2997,
"cdna_start": 1410,
"cdna_end": null,
"cdna_length": 5064,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.56G>A",
"hgvs_p": "p.Arg19Gln",
"transcript": "ENST00000492318.1",
"protein_id": "ENSP00000419317.1",
"transcript_support_level": 5,
"aa_start": 19,
"aa_end": null,
"aa_length": 188,
"cds_start": 56,
"cds_end": null,
"cds_length": 568,
"cdna_start": 58,
"cdna_end": null,
"cdna_length": 570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.827G>A",
"hgvs_p": "p.Arg276Gln",
"transcript": "XM_047447228.1",
"protein_id": "XP_047303184.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 1161,
"cds_start": 827,
"cds_end": null,
"cds_length": 3486,
"cdna_start": 1156,
"cdna_end": null,
"cdna_length": 5833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.827G>A",
"hgvs_p": "p.Arg276Gln",
"transcript": "XM_047447229.1",
"protein_id": "XP_047303185.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 1161,
"cds_start": 827,
"cds_end": null,
"cds_length": 3486,
"cdna_start": 1055,
"cdna_end": null,
"cdna_length": 5732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.707G>A",
"hgvs_p": "p.Arg236Gln",
"transcript": "XM_047447230.1",
"protein_id": "XP_047303186.1",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 1121,
"cds_start": 707,
"cds_end": null,
"cds_length": 3366,
"cdna_start": 964,
"cdna_end": null,
"cdna_length": 5641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.707G>A",
"hgvs_p": "p.Arg236Gln",
"transcript": "XM_047447231.1",
"protein_id": "XP_047303187.1",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 1121,
"cds_start": 707,
"cds_end": null,
"cds_length": 3366,
"cdna_start": 822,
"cdna_end": null,
"cdna_length": 5499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.440G>A",
"hgvs_p": "p.Arg147Gln",
"transcript": "XM_047447235.1",
"protein_id": "XP_047303191.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 1032,
"cds_start": 440,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 5262,
"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": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.1385G>A",
"hgvs_p": null,
"transcript": "XR_001739978.2",
"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": 2805,
"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": 12,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.*757G>A",
"hgvs_p": null,
"transcript": "ENST00000629124.2",
"protein_id": "ENSP00000486745.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 161,
"cds_start": -4,
"cds_end": null,
"cds_length": 486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4322,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"dbsnp": "rs1376334317",
"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": 0.8409621715545654,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.56,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9985,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000383202.7",
"gene_symbol": "STAG1",
"hgnc_id": 11354,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373Gln"
}
],
"clinvar_disease": " autosomal dominant 47,Inborn genetic diseases,Intellectual disability,STAG1-related disorder,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:2",
"phenotype_combined": "STAG1-related disorder|Intellectual disability, autosomal dominant 47|Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}