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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: 1-43439950-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=43439950&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 43439950,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000634258.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SZT2",
"gene_hgnc_id": 29040,
"hgvs_c": "c.7112A>T",
"hgvs_p": "p.Glu2371Val",
"transcript": "NM_001365999.1",
"protein_id": "NP_001352928.1",
"transcript_support_level": null,
"aa_start": 2371,
"aa_end": null,
"aa_length": 3432,
"cds_start": 7112,
"cds_end": null,
"cds_length": 10299,
"cdna_start": 7182,
"cdna_end": null,
"cdna_length": 14136,
"mane_select": "ENST00000634258.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SZT2",
"gene_hgnc_id": 29040,
"hgvs_c": "c.7112A>T",
"hgvs_p": "p.Glu2371Val",
"transcript": "ENST00000634258.3",
"protein_id": "ENSP00000489255.1",
"transcript_support_level": 5,
"aa_start": 2371,
"aa_end": null,
"aa_length": 3432,
"cds_start": 7112,
"cds_end": null,
"cds_length": 10299,
"cdna_start": 7182,
"cdna_end": null,
"cdna_length": 14136,
"mane_select": "NM_001365999.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 71,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SZT2",
"gene_hgnc_id": 29040,
"hgvs_c": "c.6941A>T",
"hgvs_p": "p.Glu2314Val",
"transcript": "NM_015284.4",
"protein_id": "NP_056099.3",
"transcript_support_level": null,
"aa_start": 2314,
"aa_end": null,
"aa_length": 3375,
"cds_start": 6941,
"cds_end": null,
"cds_length": 10128,
"cdna_start": 7011,
"cdna_end": null,
"cdna_length": 13965,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 71,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SZT2",
"gene_hgnc_id": 29040,
"hgvs_c": "c.6941A>T",
"hgvs_p": "p.Glu2314Val",
"transcript": "ENST00000562955.2",
"protein_id": "ENSP00000457168.1",
"transcript_support_level": 5,
"aa_start": 2314,
"aa_end": null,
"aa_length": 3375,
"cds_start": 6941,
"cds_end": null,
"cds_length": 10128,
"cdna_start": 7014,
"cdna_end": null,
"cdna_length": 13968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SZT2",
"gene_hgnc_id": 29040,
"hgvs_c": "n.3566A>T",
"hgvs_p": null,
"transcript": "ENST00000648058.1",
"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": 7430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SZT2",
"gene_hgnc_id": 29040,
"hgvs_c": "n.1862A>T",
"hgvs_p": null,
"transcript": "ENST00000649403.1",
"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": 5296,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SZT2",
"gene_hgnc_id": 29040,
"dbsnp": "rs1306918506",
"frequency_reference_population": 0.0000013683373,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136834,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3588091731071472,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.072,
"revel_prediction": "Benign",
"alphamissense_score": 0.561,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.387,
"phylop100way_prediction": "Uncertain_significance",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP5,BP4",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 1,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000634258.3",
"gene_symbol": "SZT2",
"hgnc_id": 29040,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.7112A>T",
"hgvs_p": "p.Glu2371Val"
}
],
"clinvar_disease": "Self-limited epilepsy with centrotemporal spikes",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Self-limited epilepsy with centrotemporal spikes",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}