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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-3243-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=M&pos=3243&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "M",
"pos": 3243,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000000000",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "G",
"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": "TRNL1",
"gene_hgnc_id": 7490,
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Glu5Gly",
"transcript": "unassigned_transcript_4788",
"protein_id": null,
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 24,
"cds_start": 14,
"cds_end": null,
"cds_length": 75,
"cdna_start": 14,
"cdna_end": null,
"cdna_length": 75,
"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-TL1",
"gene_hgnc_id": 7490,
"hgvs_c": "n.14A>G",
"hgvs_p": null,
"transcript": "ENST00000386347.1",
"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": 75,
"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-ND1",
"gene_hgnc_id": 7455,
"hgvs_c": "c.-64A>G",
"hgvs_p": null,
"transcript": "ENST00000361390.2",
"protein_id": "ENSP00000354687.2",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 956,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 956,
"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": "ND1",
"gene_hgnc_id": 7455,
"hgvs_c": "c.-64A>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_4789",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 956,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 956,
"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-RNR2",
"gene_hgnc_id": 7471,
"hgvs_c": "n.*14A>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": [
"downstream_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.*14A>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": "TRNL1",
"gene_hgnc_id": 7490,
"dbsnp": "rs199474657",
"frequency_reference_population": null,
"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": 0,
"gnomad_mito_heteroplasmic": 6,
"computational_score_selected": 13.348299980163574,
"computational_prediction_selected": "Uncertain_significance",
"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": 5.826,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": 13.348299980163574,
"mitotip_prediction": "Uncertain_significance",
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000000000",
"gene_symbol": "TRNL1",
"hgnc_id": 7490,
"effects": [
"missense_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "c.14A>G",
"hgvs_p": "p.Glu5Gly"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000386347.1",
"gene_symbol": "MT-TL1",
"hgnc_id": 7490,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.14A>G",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000361390.2",
"gene_symbol": "MT-ND1",
"hgnc_id": 7455,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,Mitochondrial",
"hgvs_c": "c.-64A>G",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000000000",
"gene_symbol": "ND1",
"hgnc_id": 7455,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,Mitochondrial",
"hgvs_c": "c.-64A>G",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000000000",
"gene_symbol": "RNR2",
"hgnc_id": 7471,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.*14A>G",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000387347.2",
"gene_symbol": "MT-RNR2",
"hgnc_id": 7471,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "Mitochondrial",
"hgvs_c": "n.*14A>G",
"hgvs_p": null
}
],
"clinvar_disease": " 1, axonal, mitochondrial, mitochondrial form, nuclear type 1,3-methylglutaconic aciduria type 1,Age related macular degeneration 2,Auditory neuropathy spectrum disorder,Cerebral palsy,Charcot-Marie-Tooth disease,Cyclical vomiting syndrome,Diabetes-deafness syndrome maternally transmitted,Glucose intolerance,Hypertrophic cardiomyopathy,Leigh Syndrome (mtDNA mutation),Leigh syndrome,MELAS syndrome,MERRF syndrome,MERRF/MELAS overlap syndrome,Maternally-inherited mitochondrial myopathy,Mitochondrial complex IV deficiency,Mitochondrial disease,See cases,Sensorineural hearing loss disorder,Short stature,Stroke disorder,not provided,not specified",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:26 LP:2 O:3",
"phenotype_combined": "MELAS-/-Leigh-Syndrome-/-DMDF-/-MIDD-/-SNHL-/-CPEO-/-MM-/-FSGS-/-ASD-/-Cardiac+multi-organ-dysfunction,MM-/-MELAS-/-SNHL-/-CPEO,MELAS syndrome|Cyclical vomiting syndrome|Age related macular degeneration 2|Mitochondrial complex IV deficiency, nuclear type 1|3-methylglutaconic aciduria type 1|MERRF/MELAS overlap syndrome|Diabetes-deafness syndrome maternally transmitted|Leigh syndrome|not provided|Mitochondrial disease|Short stature;Stroke disorder;Sensorineural hearing loss disorder;Glucose intolerance|MELAS syndrome;MERRF syndrome|Cerebral palsy|not specified|See cases|Charcot-Marie-Tooth disease, axonal, mitochondrial form, 1|Maternally-inherited mitochondrial myopathy|MELAS syndrome;Leigh Syndrome (mtDNA mutation);Hypertrophic cardiomyopathy;Diabetes-deafness syndrome maternally transmitted|Auditory neuropathy spectrum disorder|Leigh syndrome, mitochondrial",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}