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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: 16-21965440-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=21965440&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 21965440,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000268379.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UQCRC2",
"gene_hgnc_id": 12586,
"hgvs_c": "c.547C>T",
"hgvs_p": "p.Arg183Trp",
"transcript": "NM_003366.4",
"protein_id": "NP_003357.2",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 453,
"cds_start": 547,
"cds_end": null,
"cds_length": 1362,
"cdna_start": 610,
"cdna_end": null,
"cdna_length": 1914,
"mane_select": "ENST00000268379.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UQCRC2",
"gene_hgnc_id": 12586,
"hgvs_c": "c.547C>T",
"hgvs_p": "p.Arg183Trp",
"transcript": "ENST00000268379.9",
"protein_id": "ENSP00000268379.4",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 453,
"cds_start": 547,
"cds_end": null,
"cds_length": 1362,
"cdna_start": 610,
"cdna_end": null,
"cdna_length": 1914,
"mane_select": "NM_003366.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UQCRC2",
"gene_hgnc_id": 12586,
"hgvs_c": "c.547C>T",
"hgvs_p": "p.Arg183Trp",
"transcript": "ENST00000561553.5",
"protein_id": "ENSP00000456232.1",
"transcript_support_level": 5,
"aa_start": 183,
"aa_end": null,
"aa_length": 412,
"cds_start": 547,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 600,
"cdna_end": null,
"cdna_length": 1415,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UQCRC2",
"gene_hgnc_id": 12586,
"hgvs_c": "c.463C>T",
"hgvs_p": "p.Arg155Trp",
"transcript": "ENST00000565331.5",
"protein_id": "ENSP00000455088.1",
"transcript_support_level": 3,
"aa_start": 155,
"aa_end": null,
"aa_length": 175,
"cds_start": 463,
"cds_end": null,
"cds_length": 528,
"cdna_start": 500,
"cdna_end": null,
"cdna_length": 565,
"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": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UQCRC2",
"gene_hgnc_id": 12586,
"hgvs_c": "n.727C>T",
"hgvs_p": null,
"transcript": "ENST00000563711.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 2008,
"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": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UQCRC2",
"gene_hgnc_id": 12586,
"hgvs_c": "n.547C>T",
"hgvs_p": null,
"transcript": "ENST00000563898.5",
"protein_id": "ENSP00000456738.1",
"transcript_support_level": 5,
"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": 1406,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UQCRC2",
"gene_hgnc_id": 12586,
"hgvs_c": "n.219C>T",
"hgvs_p": null,
"transcript": "ENST00000567597.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDZD9",
"gene_hgnc_id": 28740,
"hgvs_c": "c.607-7823G>A",
"hgvs_p": null,
"transcript": "XM_017023109.2",
"protein_id": "XP_016878598.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDZD9",
"gene_hgnc_id": 28740,
"hgvs_c": "c.601-7823G>A",
"hgvs_p": null,
"transcript": "XM_047433888.1",
"protein_id": "XP_047289844.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 210,
"cds_start": -4,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 688,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "UQCRC2",
"gene_hgnc_id": 12586,
"dbsnp": "rs374661051",
"frequency_reference_population": 0.000008675445,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000889413,
"gnomad_genomes_af": 0.0000065741,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6302262544631958,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.336,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4478,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.199,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"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": "ENST00000268379.9",
"gene_symbol": "UQCRC2",
"hgnc_id": 12586,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.547C>T",
"hgvs_p": "p.Arg183Trp"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "XM_017023109.2",
"gene_symbol": "PDZD9",
"hgnc_id": 28740,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.607-7823G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Mitochondrial complex III deficiency nuclear type 5,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:2",
"phenotype_combined": "Mitochondrial complex III deficiency nuclear type 5|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}