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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-1555-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=1555&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "M",
"pos": 1555,
"ref": "A",
"alt": "G",
"effect": "non_coding_transcript_exon_variant",
"transcript": "unassigned_transcript_4785",
"consequences": [
{
"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-RNR1",
"gene_hgnc_id": 7470,
"hgvs_c": "n.908A>G",
"hgvs_p": null,
"transcript": "ENST00000389680.2",
"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": 954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"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": "RNR1",
"gene_hgnc_id": 7470,
"hgvs_c": "n.908A>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4785",
"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": 954,
"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": "TRNV",
"gene_hgnc_id": 7500,
"hgvs_c": "c.-47A>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4786",
"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": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MT-TV",
"gene_hgnc_id": 7500,
"hgvs_c": "n.-47A>G",
"hgvs_p": null,
"transcript": "ENST00000387342.1",
"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
},
{
"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-RNR2",
"gene_hgnc_id": 7471,
"hgvs_c": "n.-116A>G",
"hgvs_p": null,
"transcript": "ENST00000387347.2",
"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": 1559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"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": "RNR2",
"gene_hgnc_id": 7471,
"hgvs_c": "n.-116A>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4787",
"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": 1559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RNR1",
"gene_hgnc_id": 7470,
"dbsnp": "rs267606617",
"frequency_reference_population": null,
"hom_count_reference_population": 63,
"allele_count_reference_population": 63,
"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": 63,
"gnomad_mito_heteroplasmic": 11,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": 3.252,
"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": null,
"mitotip_prediction": null,
"acmg_score": 7,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS4,PP3,PS3_Moderate",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PS4",
"PP3",
"PS3_Moderate"
],
"verdict": "Pathogenic",
"transcript": "unassigned_transcript_4785",
"gene_symbol": "RNR1",
"hgnc_id": 7470,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.908A>G",
"hgvs_p": null
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PS4",
"PP3",
"PS3_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000389680.2",
"gene_symbol": "MT-RNR1",
"hgnc_id": 7470,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.908A>G",
"hgvs_p": null
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PS4",
"PP3",
"PS3_Moderate"
],
"verdict": "Pathogenic",
"transcript": "unassigned_transcript_4786",
"gene_symbol": "TRNV",
"hgnc_id": 7500,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.-47A>G",
"hgvs_p": null
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PS4",
"PP3",
"PS3_Moderate"
],
"verdict": "Pathogenic",
"transcript": "unassigned_transcript_4787",
"gene_symbol": "RNR2",
"hgnc_id": 7471,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-116A>G",
"hgvs_p": null
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PS4",
"PP3",
"PS3_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000387342.1",
"gene_symbol": "MT-TV",
"hgnc_id": 7500,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-47A>G",
"hgvs_p": null
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PS4",
"PP3",
"PS3_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000387347.2",
"gene_symbol": "MT-RNR2",
"hgnc_id": 7471,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.-116A>G",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal-mitochondrial type, sensorineural,Aminoglycoside induced ototoxicity,Aminoglycoside-induced deafness,Gentamicin response,Hearing loss,Mitochondrial disease,Mitochondrial non-syndromic sensorineural hearing loss,Rare genetic deafness,Restrictive cardiomyopathy,amikacin response - Toxicity,aminoglycoside antibacterials response - Toxicity,gentamicin response - Toxicity,kanamycin response - Toxicity,not provided,streptomycin response - Toxicity,tobramycin response - Toxicity",
"clinvar_classification": " drug response,Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:8 O:7",
"phenotype_combined": "DEAF|-autism-spectrum-intellectual-disability|-possibly-antiatherosclerotic,Aminoglycoside-induced deafness|Mitochondrial non-syndromic sensorineural hearing loss|Restrictive cardiomyopathy|not provided|Mitochondrial non-syndromic sensorineural hearing loss;Aminoglycoside-induced deafness|Gentamicin response|Rare genetic deafness|tobramycin response - Toxicity|aminoglycoside antibacterials response - Toxicity|gentamicin response - Toxicity|kanamycin response - Toxicity|amikacin response - Toxicity|streptomycin response - Toxicity|Aminoglycoside induced ototoxicity|Mitochondrial disease|Hearing loss, sensorineural, autosomal-mitochondrial type",
"pathogenicity_classification_combined": "Pathogenic; drug response",
"custom_annotations": null
}
],
"message": null
}