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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-9804-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=9804&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "M",
"pos": 9804,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000362079.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"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": "MT-CO3",
"gene_hgnc_id": 7422,
"hgvs_c": "c.598G>A",
"hgvs_p": "p.Ala200Thr",
"transcript": "ENST00000362079.2",
"protein_id": "ENSP00000354982.2",
"transcript_support_level": 6,
"aa_start": 200,
"aa_end": null,
"aa_length": 260,
"cds_start": 598,
"cds_end": null,
"cds_length": 784,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000362079.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"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": "COX3",
"gene_hgnc_id": 7422,
"hgvs_c": "c.598G>A",
"hgvs_p": "p.Ala200Thr",
"transcript": "unassigned_transcript_4806",
"protein_id": null,
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 260,
"cds_start": 598,
"cds_end": null,
"cds_length": 784,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "unassigned_transcript_4806"
},
{
"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": "TRNG",
"gene_hgnc_id": 7486,
"hgvs_c": "c.-187G>A",
"hgvs_p": null,
"transcript": "unassigned_transcript_4807",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 21,
"cds_start": null,
"cds_end": null,
"cds_length": 68,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "unassigned_transcript_4807"
},
{
"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-TG",
"gene_hgnc_id": 7486,
"hgvs_c": "n.-187G>A",
"hgvs_p": null,
"transcript": "ENST00000387429.1",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "Mt_tRNA",
"feature": "ENST00000387429.1"
}
],
"gene_symbol": "MT-CO3",
"gene_hgnc_id": 7422,
"dbsnp": "rs200613617",
"frequency_reference_population": 0.003,
"hom_count_reference_population": 181,
"allele_count_reference_population": 181,
"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": 205,
"gnomad_mito_heteroplasmic": 15,
"computational_score_selected": 0.39625030755996704,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "Apogee2",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.4109,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 4.009,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": 0.39625030755996704,
"apogee2_prediction": "Uncertain_significance",
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PS4_Moderate,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PS4_Moderate",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000362079.2",
"gene_symbol": "MT-CO3",
"hgnc_id": 7422,
"effects": [
"missense_variant"
],
"inheritance_mode": "Mitochondrial,AD,AR",
"hgvs_c": "c.598G>A",
"hgvs_p": "p.Ala200Thr"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PS4_Moderate",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "unassigned_transcript_4806",
"gene_symbol": "COX3",
"hgnc_id": 7422,
"effects": [
"missense_variant"
],
"inheritance_mode": "Mitochondrial,AD,AR",
"hgvs_c": "c.598G>A",
"hgvs_p": "p.Ala200Thr"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PS4_Moderate",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "unassigned_transcript_4807",
"gene_symbol": "TRNG",
"hgnc_id": 7486,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-187G>A",
"hgvs_p": null
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PS4_Moderate",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000387429.1",
"gene_symbol": "MT-TG",
"hgnc_id": 7486,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-187G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Leber optic atrophy,Leigh syndrome,Mitochondrial disease,See cases,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:1 US:4 B:2 O:1",
"phenotype_combined": "LHON-/-MS,Leber optic atrophy|not provided|See cases|Leigh syndrome|not specified|Mitochondrial disease",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}