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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: 3-136443368-A-ATAAAC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=136443368&ref=A&alt=ATAAAC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 136443368,
"ref": "A",
"alt": "ATAAAC",
"effect": "frameshift_variant",
"transcript": "ENST00000383202.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1460_1464dupGTTTA",
"hgvs_p": "p.Trp489fs",
"transcript": "NM_005862.3",
"protein_id": "NP_005853.2",
"transcript_support_level": null,
"aa_start": 488,
"aa_end": null,
"aa_length": 1258,
"cds_start": 1464,
"cds_end": null,
"cds_length": 3777,
"cdna_start": 1731,
"cdna_end": null,
"cdna_length": 6062,
"mane_select": "ENST00000383202.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1460_1464dupGTTTA",
"hgvs_p": "p.Trp489fs",
"transcript": "ENST00000383202.7",
"protein_id": "ENSP00000372689.2",
"transcript_support_level": 1,
"aa_start": 488,
"aa_end": null,
"aa_length": 1258,
"cds_start": 1464,
"cds_end": null,
"cds_length": 3777,
"cdna_start": 1731,
"cdna_end": null,
"cdna_length": 6062,
"mane_select": "NM_005862.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1460_1464dupGTTTA",
"hgvs_p": "p.Trp489fs",
"transcript": "ENST00000236698.9",
"protein_id": "ENSP00000236698.5",
"transcript_support_level": 1,
"aa_start": 488,
"aa_end": null,
"aa_length": 1221,
"cds_start": 1464,
"cds_end": null,
"cds_length": 3666,
"cdna_start": 1731,
"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": 18,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.*1552_*1556dupGTTTA",
"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": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.*1099_*1103dupGTTTA",
"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": 18,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.*1552_*1556dupGTTTA",
"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": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.*1099_*1103dupGTTTA",
"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": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.782_786dupGTTTA",
"hgvs_p": "p.Trp263fs",
"transcript": "ENST00000434713.6",
"protein_id": "ENSP00000404396.2",
"transcript_support_level": 5,
"aa_start": 262,
"aa_end": null,
"aa_length": 998,
"cds_start": 786,
"cds_end": null,
"cds_length": 2997,
"cdna_start": 1756,
"cdna_end": null,
"cdna_length": 5064,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.290_294dupGTTTA",
"hgvs_p": "p.Trp99fs",
"transcript": "ENST00000492318.1",
"protein_id": "ENSP00000419317.1",
"transcript_support_level": 5,
"aa_start": 98,
"aa_end": null,
"aa_length": 188,
"cds_start": 294,
"cds_end": null,
"cds_length": 568,
"cdna_start": 296,
"cdna_end": null,
"cdna_length": 570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1169_1173dupGTTTA",
"hgvs_p": "p.Trp392fs",
"transcript": "XM_047447228.1",
"protein_id": "XP_047303184.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 1161,
"cds_start": 1173,
"cds_end": null,
"cds_length": 3486,
"cdna_start": 1502,
"cdna_end": null,
"cdna_length": 5833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1169_1173dupGTTTA",
"hgvs_p": "p.Trp392fs",
"transcript": "XM_047447229.1",
"protein_id": "XP_047303185.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 1161,
"cds_start": 1173,
"cds_end": null,
"cds_length": 3486,
"cdna_start": 1401,
"cdna_end": null,
"cdna_length": 5732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1049_1053dupGTTTA",
"hgvs_p": "p.Trp352fs",
"transcript": "XM_047447230.1",
"protein_id": "XP_047303186.1",
"transcript_support_level": null,
"aa_start": 351,
"aa_end": null,
"aa_length": 1121,
"cds_start": 1053,
"cds_end": null,
"cds_length": 3366,
"cdna_start": 1310,
"cdna_end": null,
"cdna_length": 5641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.1049_1053dupGTTTA",
"hgvs_p": "p.Trp352fs",
"transcript": "XM_047447231.1",
"protein_id": "XP_047303187.1",
"transcript_support_level": null,
"aa_start": 351,
"aa_end": null,
"aa_length": 1121,
"cds_start": 1053,
"cds_end": null,
"cds_length": 3366,
"cdna_start": 1168,
"cdna_end": null,
"cdna_length": 5499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.782_786dupGTTTA",
"hgvs_p": "p.Trp263fs",
"transcript": "XM_047447235.1",
"protein_id": "XP_047303191.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 1032,
"cds_start": 786,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 931,
"cdna_end": null,
"cdna_length": 5262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LV?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.149_153dupGTTTA",
"hgvs_p": "p.Trp52fs",
"transcript": "XM_017005525.2",
"protein_id": "XP_016861014.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 821,
"cds_start": 153,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 334,
"cdna_end": null,
"cdna_length": 4665,
"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": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "n.1727_1731dupGTTTA",
"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": 16,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAG1",
"gene_hgnc_id": 11354,
"hgvs_c": "c.*1099_*1103dupGTTTA",
"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": "rs1553722294",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.438,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000383202.7",
"gene_symbol": "STAG1",
"hgnc_id": 11354,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1460_1464dupGTTTA",
"hgvs_p": "p.Trp489fs"
}
],
"clinvar_disease": " autosomal dominant 47,Intellectual disability,STAG1-related disorder",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Intellectual disability, autosomal dominant 47|STAG1-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}