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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: 5-110761547-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=110761547&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 110761547,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000355943.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "c.1022T>C",
"hgvs_p": "p.Leu341Pro",
"transcript": "NM_138773.4",
"protein_id": "NP_620128.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 418,
"cds_start": 1022,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 1135,
"cdna_end": null,
"cdna_length": 4745,
"mane_select": "ENST00000355943.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "c.1022T>C",
"hgvs_p": "p.Leu341Pro",
"transcript": "ENST00000355943.8",
"protein_id": "ENSP00000348211.3",
"transcript_support_level": 1,
"aa_start": 341,
"aa_end": null,
"aa_length": 418,
"cds_start": 1022,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 1135,
"cdna_end": null,
"cdna_length": 4745,
"mane_select": "NM_138773.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "c.779T>C",
"hgvs_p": "p.Leu260Pro",
"transcript": "NM_001303249.3",
"protein_id": "NP_001290178.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 337,
"cds_start": 779,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 892,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "c.779T>C",
"hgvs_p": "p.Leu260Pro",
"transcript": "ENST00000447245.6",
"protein_id": "ENSP00000399717.2",
"transcript_support_level": 2,
"aa_start": 260,
"aa_end": null,
"aa_length": 337,
"cds_start": 779,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 858,
"cdna_end": null,
"cdna_length": 1575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "c.749T>C",
"hgvs_p": "p.Leu250Pro",
"transcript": "NM_001303250.3",
"protein_id": "NP_001290179.1",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 327,
"cds_start": 749,
"cds_end": null,
"cds_length": 984,
"cdna_start": 842,
"cdna_end": null,
"cdna_length": 4452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "c.584T>C",
"hgvs_p": "p.Leu195Pro",
"transcript": "ENST00000504098.1",
"protein_id": "ENSP00000425708.1",
"transcript_support_level": 5,
"aa_start": 195,
"aa_end": null,
"aa_length": 272,
"cds_start": 584,
"cds_end": null,
"cds_length": 819,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 2345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "c.536T>C",
"hgvs_p": "p.Leu179Pro",
"transcript": "ENST00000513807.5",
"protein_id": "ENSP00000421134.1",
"transcript_support_level": 2,
"aa_start": 179,
"aa_end": null,
"aa_length": 256,
"cds_start": 536,
"cds_end": null,
"cds_length": 771,
"cdna_start": 826,
"cdna_end": null,
"cdna_length": 1546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "c.383T>C",
"hgvs_p": "p.Leu128Pro",
"transcript": "ENST00000509432.1",
"protein_id": "ENSP00000426604.1",
"transcript_support_level": 2,
"aa_start": 128,
"aa_end": null,
"aa_length": 205,
"cds_start": 383,
"cds_end": null,
"cds_length": 618,
"cdna_start": 930,
"cdna_end": null,
"cdna_length": 1596,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "n.1338T>C",
"hgvs_p": null,
"transcript": "ENST00000502462.6",
"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": 1446,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "n.2622T>C",
"hgvs_p": null,
"transcript": "ENST00000513706.2",
"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": 6236,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"hgvs_c": "n.1261T>C",
"hgvs_p": null,
"transcript": "NR_138151.2",
"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": 4871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC25A46",
"gene_hgnc_id": 25198,
"dbsnp": "rs1057519294",
"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": 0.9755432605743408,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.926,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9992,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.42,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.218,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000355943.8",
"gene_symbol": "SLC25A46",
"hgnc_id": 25198,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1022T>C",
"hgvs_p": "p.Leu341Pro"
}
],
"clinvar_disease": " type 1E,Pontocerebellar hypoplasia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Pontocerebellar hypoplasia, type 1E",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}