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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: 19-3008902-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=3008902&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 3008902,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000262953.11",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Ser406Phe",
"transcript": "NM_003260.5",
"protein_id": "NP_003251.2",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 743,
"cds_start": 1217,
"cds_end": null,
"cds_length": 2232,
"cdna_start": 1593,
"cdna_end": null,
"cdna_length": 2812,
"mane_select": "ENST00000262953.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Ser406Phe",
"transcript": "ENST00000262953.11",
"protein_id": "ENSP00000262953.5",
"transcript_support_level": 1,
"aa_start": 406,
"aa_end": null,
"aa_length": 743,
"cds_start": 1217,
"cds_end": null,
"cds_length": 2232,
"cdna_start": 1593,
"cdna_end": null,
"cdna_length": 2812,
"mane_select": "NM_003260.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.1220C>T",
"hgvs_p": "p.Ser407Phe",
"transcript": "ENST00000590536.5",
"protein_id": "ENSP00000466542.1",
"transcript_support_level": 1,
"aa_start": 407,
"aa_end": null,
"aa_length": 744,
"cds_start": 1220,
"cds_end": null,
"cds_length": 2235,
"cdna_start": 1329,
"cdna_end": null,
"cdna_length": 2344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.1259C>T",
"hgvs_p": "p.Ser420Phe",
"transcript": "ENST00000591529.5",
"protein_id": "ENSP00000468279.1",
"transcript_support_level": 1,
"aa_start": 420,
"aa_end": null,
"aa_length": 706,
"cds_start": 1259,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 1343,
"cdna_end": null,
"cdna_length": 2483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.1220C>T",
"hgvs_p": "p.Ser407Phe",
"transcript": "NM_001300846.2",
"protein_id": "NP_001287775.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 744,
"cds_start": 1220,
"cds_end": null,
"cds_length": 2235,
"cdna_start": 1596,
"cdna_end": null,
"cdna_length": 2815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.1259C>T",
"hgvs_p": "p.Ser420Phe",
"transcript": "NM_001144761.2",
"protein_id": "NP_001138233.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 706,
"cds_start": 1259,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 1343,
"cdna_end": null,
"cdna_length": 2485,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.1259C>T",
"hgvs_p": "p.Ser420Phe",
"transcript": "ENST00000426948.6",
"protein_id": "ENSP00000392869.2",
"transcript_support_level": 5,
"aa_start": 420,
"aa_end": null,
"aa_length": 706,
"cds_start": 1259,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 1259,
"cdna_end": null,
"cdna_length": 2406,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.851C>T",
"hgvs_p": "p.Ser284Phe",
"transcript": "NM_001144762.2",
"protein_id": "NP_001138234.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 621,
"cds_start": 851,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 1065,
"cdna_end": null,
"cdna_length": 2284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.851C>T",
"hgvs_p": "p.Ser284Phe",
"transcript": "ENST00000443826.7",
"protein_id": "ENSP00000392427.2",
"transcript_support_level": 2,
"aa_start": 284,
"aa_end": null,
"aa_length": 621,
"cds_start": 851,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 1057,
"cdna_end": null,
"cdna_length": 2238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Ser54Phe",
"transcript": "ENST00000589364.5",
"protein_id": "ENSP00000465292.1",
"transcript_support_level": 5,
"aa_start": 54,
"aa_end": null,
"aa_length": 278,
"cds_start": 161,
"cds_end": null,
"cds_length": 839,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.1184C>T",
"hgvs_p": "p.Ser395Phe",
"transcript": "XM_011528230.2",
"protein_id": "XP_011526532.1",
"transcript_support_level": null,
"aa_start": 395,
"aa_end": null,
"aa_length": 732,
"cds_start": 1184,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 1560,
"cdna_end": null,
"cdna_length": 2779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.1220C>T",
"hgvs_p": "p.Ser407Phe",
"transcript": "XM_006722864.3",
"protein_id": "XP_006722927.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 693,
"cds_start": 1220,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 1596,
"cdna_end": null,
"cdna_length": 2738,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "c.256+10510C>T",
"hgvs_p": null,
"transcript": "ENST00000586422.5",
"protein_id": "ENSP00000465519.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 119,
"cds_start": -4,
"cds_end": null,
"cds_length": 360,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"hgvs_c": "n.-26C>T",
"hgvs_p": null,
"transcript": "ENST00000586492.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 331,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TLE2",
"gene_hgnc_id": 11838,
"dbsnp": "rs200222446",
"frequency_reference_population": 0.00002820231,
"hom_count_reference_population": 0,
"allele_count_reference_population": 45,
"gnomad_exomes_af": 0.0000117784,
"gnomad_genomes_af": 0.000183852,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 28,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08057466149330139,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.189,
"revel_prediction": "Benign",
"alphamissense_score": 0.1282,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.77,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.04,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000262953.11",
"gene_symbol": "TLE2",
"hgnc_id": 11838,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1217C>T",
"hgvs_p": "p.Ser406Phe"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}