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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-10197-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=10197&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "M",
"pos": 10197,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000361227.2",
"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-ND3",
"gene_hgnc_id": 7458,
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Ala47Thr",
"transcript": "ENST00000361227.2",
"protein_id": "ENSP00000355206.2",
"transcript_support_level": 6,
"aa_start": 47,
"aa_end": null,
"aa_length": 114,
"cds_start": 139,
"cds_end": null,
"cds_length": 346,
"cdna_start": 139,
"cdna_end": null,
"cdna_length": 346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "ND3",
"gene_hgnc_id": 7458,
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Ala47Thr",
"transcript": "unassigned_transcript_4808",
"protein_id": null,
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 114,
"cds_start": 139,
"cds_end": null,
"cds_length": 346,
"cdna_start": 139,
"cdna_end": null,
"cdna_length": 346,
"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-CO3",
"gene_hgnc_id": 7422,
"hgvs_c": "c.*207G>A",
"hgvs_p": null,
"transcript": "ENST00000362079.2",
"protein_id": "ENSP00000354982.2",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 260,
"cds_start": -4,
"cds_end": null,
"cds_length": 784,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 784,
"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": "TRNR",
"gene_hgnc_id": 7496,
"hgvs_c": "c.-208G>A",
"hgvs_p": null,
"transcript": "unassigned_transcript_4809",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 20,
"cds_start": -4,
"cds_end": null,
"cds_length": 65,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 65,
"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-TR",
"gene_hgnc_id": 7496,
"hgvs_c": "n.-208G>A",
"hgvs_p": null,
"transcript": "ENST00000387439.1",
"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": 65,
"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": "COX3",
"gene_hgnc_id": 7422,
"hgvs_c": "c.*207G>A",
"hgvs_p": null,
"transcript": "unassigned_transcript_4806",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 260,
"cds_start": -4,
"cds_end": null,
"cds_length": 784,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 784,
"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": "TRNG",
"gene_hgnc_id": 7486,
"hgvs_c": "c.*139G>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": -4,
"cds_end": null,
"cds_length": 68,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 68,
"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-TG",
"gene_hgnc_id": 7486,
"hgvs_c": "n.*139G>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 68,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MT-ND3",
"gene_hgnc_id": 7458,
"dbsnp": "rs267606891",
"frequency_reference_population": null,
"hom_count_reference_population": null,
"allele_count_reference_population": null,
"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": 0.843686044216156,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "Apogee2",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.2513,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 4.687,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": 0.843686044216156,
"apogee2_prediction": "Pathogenic",
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM6,PS4,PP1_Moderate,PS3_Supporting,PP3,PM2_Supporting",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM6",
"PS4",
"PP1_Moderate",
"PS3_Supporting",
"PP3",
"PM2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "ENST00000361227.2",
"gene_symbol": "MT-ND3",
"hgnc_id": 7458,
"effects": [
"missense_variant"
],
"inheritance_mode": "Mitochondrial,AR",
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Ala47Thr"
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM6",
"PS4",
"PP1_Moderate",
"PS3_Supporting",
"PP3",
"PM2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "unassigned_transcript_4808",
"gene_symbol": "ND3",
"hgnc_id": 7458,
"effects": [
"missense_variant"
],
"inheritance_mode": "Mitochondrial,AR",
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Ala47Thr"
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM6",
"PS4",
"PP1_Moderate",
"PS3_Supporting",
"PP3",
"PM2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "ENST00000362079.2",
"gene_symbol": "MT-CO3",
"hgnc_id": 7422,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AD,AR",
"hgvs_c": "c.*207G>A",
"hgvs_p": null
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM6",
"PS4",
"PP1_Moderate",
"PS3_Supporting",
"PP3",
"PM2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "unassigned_transcript_4809",
"gene_symbol": "TRNR",
"hgnc_id": 7496,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-208G>A",
"hgvs_p": null
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM6",
"PS4",
"PP1_Moderate",
"PS3_Supporting",
"PP3",
"PM2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "ENST00000387439.1",
"gene_symbol": "MT-TR",
"hgnc_id": 7496,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-208G>A",
"hgvs_p": null
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM6",
"PS4",
"PP1_Moderate",
"PS3_Supporting",
"PP3",
"PM2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "unassigned_transcript_4806",
"gene_symbol": "COX3",
"hgnc_id": 7422,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AD,AR",
"hgvs_c": "c.*207G>A",
"hgvs_p": null
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM6",
"PS4",
"PP1_Moderate",
"PS3_Supporting",
"PP3",
"PM2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "unassigned_transcript_4807",
"gene_symbol": "TRNG",
"hgnc_id": 7486,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.*139G>A",
"hgvs_p": null
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM6",
"PS4",
"PP1_Moderate",
"PS3_Supporting",
"PP3",
"PM2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "ENST00000387429.1",
"gene_symbol": "MT-TG",
"hgnc_id": 7486,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.*139G>A",
"hgvs_p": null
}
],
"clinvar_disease": " episodic, mitochondrial type 1, with optic atrophy and reversible leukoencephalopathy,Leber optic atrophy and dystonia,Leigh syndrome,Mitochondrial DNA-Associated Leigh Syndrome and NARP,Mitochondrial complex I deficiency,Mitochondrial disease,Mitochondrial myopathy,See cases,not provided,not specified",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:6 LP:2 O:1",
"phenotype_combined": "Leigh-Disease-/-Dystonia-/-Stroke-/-LDYT,Leigh-Disease,Leber optic atrophy and dystonia|Mitochondrial complex I deficiency, mitochondrial type 1|Mitochondrial DNA-Associated Leigh Syndrome and NARP|Leigh syndrome|not specified|Mitochondrial disease|not provided|See cases|Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}