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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: 2-199348874-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=199348874&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 199348874,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000417098.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Ala334Thr",
"transcript": "NM_001172509.2",
"protein_id": "NP_001165980.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 733,
"cds_start": 1000,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1660,
"cdna_end": null,
"cdna_length": 5568,
"mane_select": "ENST00000417098.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Ala334Thr",
"transcript": "ENST00000417098.6",
"protein_id": "ENSP00000401112.1",
"transcript_support_level": 2,
"aa_start": 334,
"aa_end": null,
"aa_length": 733,
"cds_start": 1000,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1660,
"cdna_end": null,
"cdna_length": 5568,
"mane_select": "NM_001172509.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Ala334Thr",
"transcript": "ENST00000260926.9",
"protein_id": "ENSP00000260926.5",
"transcript_support_level": 1,
"aa_start": 334,
"aa_end": null,
"aa_length": 733,
"cds_start": 1000,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 5318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.646G>A",
"hgvs_p": "p.Ala216Thr",
"transcript": "ENST00000428695.6",
"protein_id": "ENSP00000388581.1",
"transcript_support_level": 1,
"aa_start": 216,
"aa_end": null,
"aa_length": 615,
"cds_start": 646,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 875,
"cdna_end": null,
"cdna_length": 2313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Ala334Thr",
"transcript": "NM_001172517.1",
"protein_id": "NP_001165988.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 733,
"cds_start": 1000,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 5326,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Ala334Thr",
"transcript": "NM_015265.4",
"protein_id": "NP_056080.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 733,
"cds_start": 1000,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1393,
"cdna_end": null,
"cdna_length": 5301,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Ala334Thr",
"transcript": "ENST00000457245.5",
"protein_id": "ENSP00000405420.1",
"transcript_support_level": 2,
"aa_start": 334,
"aa_end": null,
"aa_length": 733,
"cds_start": 1000,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1393,
"cdna_end": null,
"cdna_length": 2656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Ala334Thr",
"transcript": "ENST00000700193.1",
"protein_id": "ENSP00000514854.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 733,
"cds_start": 1000,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1261,
"cdna_end": null,
"cdna_length": 3175,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.823G>A",
"hgvs_p": "p.Ala275Thr",
"transcript": "ENST00000443023.5",
"protein_id": "ENSP00000388764.1",
"transcript_support_level": 5,
"aa_start": 275,
"aa_end": null,
"aa_length": 674,
"cds_start": 823,
"cds_end": null,
"cds_length": 2025,
"cdna_start": 2289,
"cdna_end": null,
"cdna_length": 6194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.646G>A",
"hgvs_p": "p.Ala216Thr",
"transcript": "ENST00000700191.1",
"protein_id": "ENSP00000514853.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 615,
"cds_start": 646,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 849,
"cdna_end": null,
"cdna_length": 4749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.652G>A",
"hgvs_p": "p.Ala218Thr",
"transcript": "ENST00000700210.1",
"protein_id": "ENSP00000514861.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 486,
"cds_start": 652,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 654,
"cdna_end": null,
"cdna_length": 2281,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Ala334Thr",
"transcript": "XM_047443775.1",
"protein_id": "XP_047299731.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 733,
"cds_start": 1000,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 1144,
"cdna_end": null,
"cdna_length": 5057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.826G>A",
"hgvs_p": "p.Ala276Thr",
"transcript": "XM_005246396.4",
"protein_id": "XP_005246453.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 675,
"cds_start": 826,
"cds_end": null,
"cds_length": 2028,
"cdna_start": 916,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "n.639G>A",
"hgvs_p": null,
"transcript": "ENST00000483346.2",
"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": 2647,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SATB2",
"gene_hgnc_id": 21637,
"hgvs_c": "c.347-76202G>A",
"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": "rs754385480",
"frequency_reference_population": 0.000004956679,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000478845,
"gnomad_genomes_af": 0.00000657324,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.17663195729255676,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.112,
"revel_prediction": "Benign",
"alphamissense_score": 0.1046,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.632,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000417098.6",
"gene_symbol": "SATB2",
"hgnc_id": 21637,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Ala334Thr"
}
],
"clinvar_disease": "Chromosome 2q32-q33 deletion syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Chromosome 2q32-q33 deletion syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}