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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: M-12258-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=12258&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "M",
"pos": 12258,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000000000",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNS2",
"gene_hgnc_id": 7498,
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Leu18Phe",
"transcript": "unassigned_transcript_4813",
"protein_id": null,
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 18,
"cds_start": 52,
"cds_end": null,
"cds_length": 59,
"cdna_start": 52,
"cdna_end": null,
"cdna_length": 59,
"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": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TS2",
"gene_hgnc_id": 7498,
"hgvs_c": "n.52C>T",
"hgvs_p": null,
"transcript": "ENST00000387449.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 59,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-ND5",
"gene_hgnc_id": 7461,
"hgvs_c": "c.-79C>T",
"hgvs_p": null,
"transcript": "ENST00000361567.2",
"protein_id": "ENSP00000354813.2",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 603,
"cds_start": -4,
"cds_end": null,
"cds_length": 1812,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-ND4",
"gene_hgnc_id": 7459,
"hgvs_c": "c.*121C>T",
"hgvs_p": null,
"transcript": "ENST00000361381.2",
"protein_id": "ENSP00000354961.2",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 458,
"cds_start": -4,
"cds_end": null,
"cds_length": 1378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ND5",
"gene_hgnc_id": 7461,
"hgvs_c": "c.-79C>T",
"hgvs_p": null,
"transcript": "unassigned_transcript_4815",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 603,
"cds_start": -4,
"cds_end": null,
"cds_length": 1812,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNL2",
"gene_hgnc_id": 7491,
"hgvs_c": "c.-8C>T",
"hgvs_p": null,
"transcript": "unassigned_transcript_4814",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 22,
"cds_start": -4,
"cds_end": null,
"cds_length": 71,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 71,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TL2",
"gene_hgnc_id": 7491,
"hgvs_c": "n.-8C>T",
"hgvs_p": null,
"transcript": "ENST00000387456.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 71,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ND4",
"gene_hgnc_id": 7459,
"hgvs_c": "c.*121C>T",
"hgvs_p": null,
"transcript": "unassigned_transcript_4811",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 458,
"cds_start": -4,
"cds_end": null,
"cds_length": 1378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNH",
"gene_hgnc_id": 7487,
"hgvs_c": "c.*52C>T",
"hgvs_p": null,
"transcript": "unassigned_transcript_4812",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 22,
"cds_start": -4,
"cds_end": null,
"cds_length": 69,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 69,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TH",
"gene_hgnc_id": 7487,
"hgvs_c": "n.*52C>T",
"hgvs_p": null,
"transcript": "ENST00000387441.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 69,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRNS2",
"gene_hgnc_id": 7498,
"dbsnp": "rs118203888",
"frequency_reference_population": 0,
"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": 17.162700653076172,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "Mitotip",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.09,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": 17.162700653076172,
"mitotip_prediction": "Pathogenic",
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "TRNS2",
"hgnc_id": 7498,
"effects": [
"missense_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Leu18Phe"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000387449.1",
"gene_symbol": "MT-TS2",
"hgnc_id": 7498,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.52C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000361567.2",
"gene_symbol": "MT-ND5",
"hgnc_id": 7461,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-79C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000361381.2",
"gene_symbol": "MT-ND4",
"hgnc_id": 7459,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.*121C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "ND5",
"hgnc_id": 7461,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-79C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "TRNL2",
"hgnc_id": 7491,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-8C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000387456.1",
"gene_symbol": "MT-TL2",
"hgnc_id": 7491,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-8C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "ND4",
"hgnc_id": 7459,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.*121C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000000000",
"gene_symbol": "TRNH",
"hgnc_id": 7487,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.*52C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000387441.1",
"gene_symbol": "MT-TH",
"hgnc_id": 7487,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.*52C>T",
"hgvs_p": null
}
],
"clinvar_disease": "MELAS syndrome,Mitochondrial disease",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:1 LP:1 US:1",
"phenotype_combined": "DMDF-/-RP+SNHL,Unspecified-patient-from-clinical-lab,MELAS syndrome|Mitochondrial disease",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}