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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: 12-4685324-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=4685324&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 4685324,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000266544.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFA9",
"gene_hgnc_id": 7693,
"hgvs_c": "c.962G>A",
"hgvs_p": "p.Arg321Gln",
"transcript": "NM_005002.5",
"protein_id": "NP_004993.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 377,
"cds_start": 962,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 975,
"cdna_end": null,
"cdna_length": 8356,
"mane_select": "ENST00000266544.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFA9",
"gene_hgnc_id": 7693,
"hgvs_c": "c.962G>A",
"hgvs_p": "p.Arg321Gln",
"transcript": "ENST00000266544.10",
"protein_id": "ENSP00000266544.5",
"transcript_support_level": 1,
"aa_start": 321,
"aa_end": null,
"aa_length": 377,
"cds_start": 962,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 975,
"cdna_end": null,
"cdna_length": 8356,
"mane_select": "NM_005002.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255639",
"gene_hgnc_id": null,
"hgvs_c": "c.962G>A",
"hgvs_p": "p.Arg321Gln",
"transcript": "ENST00000648836.1",
"protein_id": "ENSP00000497305.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 567,
"cds_start": 962,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 988,
"cdna_end": null,
"cdna_length": 3317,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFA9",
"gene_hgnc_id": 7693,
"hgvs_c": "c.239G>A",
"hgvs_p": "p.Arg80Gln",
"transcript": "ENST00000540688.1",
"protein_id": "ENSP00000439818.1",
"transcript_support_level": 2,
"aa_start": 80,
"aa_end": null,
"aa_length": 136,
"cds_start": 239,
"cds_end": null,
"cds_length": 411,
"cdna_start": 345,
"cdna_end": null,
"cdna_length": 642,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255639",
"gene_hgnc_id": null,
"hgvs_c": "n.239G>A",
"hgvs_p": null,
"transcript": "ENST00000544741.2",
"protein_id": "ENSP00000456318.2",
"transcript_support_level": 3,
"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": 770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255639",
"gene_hgnc_id": null,
"hgvs_c": "n.589+3024G>A",
"hgvs_p": null,
"transcript": "ENST00000543979.1",
"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": 864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NDUFA9",
"gene_hgnc_id": 7693,
"dbsnp": "rs199592341",
"frequency_reference_population": 0.00003037637,
"hom_count_reference_population": 0,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000308047,
"gnomad_genomes_af": 0.0000262674,
"gnomad_exomes_ac": 45,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3359135389328003,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.40799999237060547,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.51,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1699,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.993,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0217459599324464,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM5,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000266544.10",
"gene_symbol": "NDUFA9",
"hgnc_id": 7693,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.962G>A",
"hgvs_p": "p.Arg321Gln"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000648836.1",
"gene_symbol": "ENSG00000255639",
"hgnc_id": null,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.962G>A",
"hgvs_p": "p.Arg321Gln"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}