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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-7471-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=7471&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "M",
"pos": 7471,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000000000",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": null,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRNS1",
"gene_hgnc_id": 7497,
"hgvs_c": "c.44G>A",
"hgvs_p": "p.Trp15*",
"transcript": "unassigned_transcript_4800",
"protein_id": null,
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 22,
"cds_start": 44,
"cds_end": null,
"cds_length": 69,
"cdna_start": 44,
"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": false,
"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-TS1",
"gene_hgnc_id": 7497,
"hgvs_c": "n.44G>A",
"hgvs_p": null,
"transcript": "ENST00000387416.2",
"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
},
{
"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-CO2",
"gene_hgnc_id": 7421,
"hgvs_c": "c.-115C>T",
"hgvs_p": null,
"transcript": "ENST00000361739.1",
"protein_id": "ENSP00000354876.1",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": -4,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 684,
"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-CO1",
"gene_hgnc_id": 7419,
"hgvs_c": "c.*26C>T",
"hgvs_p": null,
"transcript": "ENST00000361624.2",
"protein_id": "ENSP00000354499.2",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 513,
"cds_start": -4,
"cds_end": null,
"cds_length": 1542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1542,
"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": "COX2",
"gene_hgnc_id": 7421,
"hgvs_c": "c.-115C>T",
"hgvs_p": null,
"transcript": "unassigned_transcript_4802",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": -4,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 684,
"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": "TRND",
"gene_hgnc_id": 7478,
"hgvs_c": "c.-47C>T",
"hgvs_p": null,
"transcript": "unassigned_transcript_4801",
"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": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TD",
"gene_hgnc_id": 7478,
"hgvs_c": "n.-47C>T",
"hgvs_p": null,
"transcript": "ENST00000387419.1",
"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
},
{
"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": "COX1",
"gene_hgnc_id": 7419,
"hgvs_c": "c.*26C>T",
"hgvs_p": null,
"transcript": "unassigned_transcript_4799",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 513,
"cds_start": -4,
"cds_end": null,
"cds_length": 1542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRNS1",
"gene_hgnc_id": 7497,
"dbsnp": "rs397515726",
"frequency_reference_population": 0.0002,
"hom_count_reference_population": 15,
"allele_count_reference_population": 15,
"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": 12,
"gnomad_mito_heteroplasmic": 0,
"computational_score_selected": 2.634079933166504,
"computational_prediction_selected": "Benign",
"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": -3.325,
"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": 2.634079933166504,
"mitotip_prediction": "Benign",
"acmg_score": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000000000",
"gene_symbol": "TRNS1",
"hgnc_id": 7497,
"effects": [
"stop_gained"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.44G>A",
"hgvs_p": "p.Trp15*"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000387416.2",
"gene_symbol": "MT-TS1",
"hgnc_id": 7497,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.44G>A",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000361739.1",
"gene_symbol": "MT-CO2",
"hgnc_id": 7421,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,Mitochondrial",
"hgvs_c": "c.-115C>T",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000361624.2",
"gene_symbol": "MT-CO1",
"hgnc_id": 7419,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AR,AD",
"hgvs_c": "c.*26C>T",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000000000",
"gene_symbol": "COX2",
"hgnc_id": 7421,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,Mitochondrial",
"hgvs_c": "c.-115C>T",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000000000",
"gene_symbol": "TRND",
"hgnc_id": 7478,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-47C>T",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000387419.1",
"gene_symbol": "MT-TD",
"hgnc_id": 7478,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-47C>T",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000000000",
"gene_symbol": "COX1",
"hgnc_id": 7419,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial,AR,AD",
"hgvs_c": "c.*26C>T",
"hgvs_p": null
}
],
"clinvar_disease": "MELAS syndrome,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"phenotype_combined": "not specified|MELAS syndrome",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}