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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: 2-199272562-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=199272562&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 199272562,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000417098.6",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1851T>C",
"hgvs_p": "p.Ser617Ser",
"transcript": "NM_001172509.2",
"protein_id": "NP_001165980.1",
"transcript_support_level": null,
"aa_start": 617,
"aa_end": null,
"aa_length": 733,
"cds_start": 1851,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2511,
"cdna_end": null,
"cdna_length": 5568,
"mane_select": "ENST00000417098.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1851T>C",
"hgvs_p": "p.Ser617Ser",
"transcript": "ENST00000417098.6",
"protein_id": "ENSP00000401112.1",
"transcript_support_level": 2,
"aa_start": 617,
"aa_end": null,
"aa_length": 733,
"cds_start": 1851,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2511,
"cdna_end": null,
"cdna_length": 5568,
"mane_select": "NM_001172509.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1851T>C",
"hgvs_p": "p.Ser617Ser",
"transcript": "ENST00000260926.9",
"protein_id": "ENSP00000260926.5",
"transcript_support_level": 1,
"aa_start": 617,
"aa_end": null,
"aa_length": 733,
"cds_start": 1851,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2264,
"cdna_end": null,
"cdna_length": 5318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1497T>C",
"hgvs_p": "p.Ser499Ser",
"transcript": "ENST00000428695.6",
"protein_id": "ENSP00000388581.1",
"transcript_support_level": 1,
"aa_start": 499,
"aa_end": null,
"aa_length": 615,
"cds_start": 1497,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 1726,
"cdna_end": null,
"cdna_length": 2313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1851T>C",
"hgvs_p": "p.Ser617Ser",
"transcript": "NM_001172517.1",
"protein_id": "NP_001165988.1",
"transcript_support_level": null,
"aa_start": 617,
"aa_end": null,
"aa_length": 733,
"cds_start": 1851,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2264,
"cdna_end": null,
"cdna_length": 5326,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1851T>C",
"hgvs_p": "p.Ser617Ser",
"transcript": "NM_015265.4",
"protein_id": "NP_056080.1",
"transcript_support_level": null,
"aa_start": 617,
"aa_end": null,
"aa_length": 733,
"cds_start": 1851,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2244,
"cdna_end": null,
"cdna_length": 5301,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1851T>C",
"hgvs_p": "p.Ser617Ser",
"transcript": "ENST00000457245.5",
"protein_id": "ENSP00000405420.1",
"transcript_support_level": 2,
"aa_start": 617,
"aa_end": null,
"aa_length": 733,
"cds_start": 1851,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2244,
"cdna_end": null,
"cdna_length": 2656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1851T>C",
"hgvs_p": "p.Ser617Ser",
"transcript": "ENST00000700193.1",
"protein_id": "ENSP00000514854.1",
"transcript_support_level": null,
"aa_start": 617,
"aa_end": null,
"aa_length": 733,
"cds_start": 1851,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2112,
"cdna_end": null,
"cdna_length": 3175,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1674T>C",
"hgvs_p": "p.Ser558Ser",
"transcript": "ENST00000443023.5",
"protein_id": "ENSP00000388764.1",
"transcript_support_level": 5,
"aa_start": 558,
"aa_end": null,
"aa_length": 674,
"cds_start": 1674,
"cds_end": null,
"cds_length": 2025,
"cdna_start": 3140,
"cdna_end": null,
"cdna_length": 6194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1497T>C",
"hgvs_p": "p.Ser499Ser",
"transcript": "ENST00000700191.1",
"protein_id": "ENSP00000514853.1",
"transcript_support_level": null,
"aa_start": 499,
"aa_end": null,
"aa_length": 615,
"cds_start": 1497,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 1700,
"cdna_end": null,
"cdna_length": 4749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1851T>C",
"hgvs_p": "p.Ser617Ser",
"transcript": "XM_047443775.1",
"protein_id": "XP_047299731.1",
"transcript_support_level": null,
"aa_start": 617,
"aa_end": null,
"aa_length": 733,
"cds_start": 1851,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1995,
"cdna_end": null,
"cdna_length": 5057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1677T>C",
"hgvs_p": "p.Ser559Ser",
"transcript": "XM_005246396.4",
"protein_id": "XP_005246453.1",
"transcript_support_level": null,
"aa_start": 559,
"aa_end": null,
"aa_length": 675,
"cds_start": 1677,
"cds_end": null,
"cds_length": 2028,
"cdna_start": 1767,
"cdna_end": null,
"cdna_length": 4829,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "n.940T>C",
"hgvs_p": null,
"transcript": "ENST00000700192.1",
"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": 3781,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "n.759T>C",
"hgvs_p": null,
"transcript": "ENST00000700207.1",
"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": 3770,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "n.796T>C",
"hgvs_p": null,
"transcript": "ENST00000700209.1",
"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": 2286,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.*100T>C",
"hgvs_p": null,
"transcript": "ENST00000700208.1",
"protein_id": "ENSP00000514860.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 118,
"cds_start": -4,
"cds_end": null,
"cds_length": 357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3515,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"dbsnp": "rs188200171",
"frequency_reference_population": 0.000031595693,
"hom_count_reference_population": 1,
"allele_count_reference_population": 51,
"gnomad_exomes_af": 0.0000314664,
"gnomad_genomes_af": 0.0000328373,
"gnomad_exomes_ac": 46,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5400000214576721,
"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": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.552,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000417098.6",
"gene_symbol": "SATB2",
"hgnc_id": 21637,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1851T>C",
"hgvs_p": "p.Ser617Ser"
}
],
"clinvar_disease": "Chromosome 2q32-q33 deletion syndrome,Inborn genetic diseases,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3",
"phenotype_combined": "Chromosome 2q32-q33 deletion syndrome|Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}