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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: 5-39341267-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=39341267&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 39341267,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000263408.5",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C9",
"gene_hgnc_id": 1358,
"hgvs_c": "c.355T>G",
"hgvs_p": "p.Cys119Gly",
"transcript": "NM_001737.5",
"protein_id": "NP_001728.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 559,
"cds_start": 355,
"cds_end": null,
"cds_length": 1680,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 2770,
"mane_select": "ENST00000263408.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C9",
"gene_hgnc_id": 1358,
"hgvs_c": "c.355T>G",
"hgvs_p": "p.Cys119Gly",
"transcript": "ENST00000263408.5",
"protein_id": "ENSP00000263408.4",
"transcript_support_level": 1,
"aa_start": 119,
"aa_end": null,
"aa_length": 559,
"cds_start": 355,
"cds_end": null,
"cds_length": 1680,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 2770,
"mane_select": "NM_001737.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C9",
"gene_hgnc_id": 1358,
"hgvs_c": "c.283T>G",
"hgvs_p": "p.Cys95Gly",
"transcript": "ENST00000509186.6",
"protein_id": "ENSP00000512235.1",
"transcript_support_level": 3,
"aa_start": 95,
"aa_end": null,
"aa_length": 535,
"cds_start": 283,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 360,
"cdna_end": null,
"cdna_length": 2744,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C9",
"gene_hgnc_id": 1358,
"hgvs_c": "c.355T>G",
"hgvs_p": "p.Cys119Gly",
"transcript": "ENST00000695880.1",
"protein_id": "ENSP00000512236.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 516,
"cds_start": 355,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 2553,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C9",
"gene_hgnc_id": 1358,
"hgvs_c": "n.386T>G",
"hgvs_p": null,
"transcript": "ENST00000467285.1",
"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": 572,
"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": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C9",
"gene_hgnc_id": 1358,
"hgvs_c": "n.355T>G",
"hgvs_p": null,
"transcript": "ENST00000695881.1",
"protein_id": "ENSP00000512237.1",
"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": 2726,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C9",
"gene_hgnc_id": 1358,
"hgvs_c": "n.386T>G",
"hgvs_p": null,
"transcript": "ENST00000695883.1",
"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": 1459,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289699",
"gene_hgnc_id": null,
"hgvs_c": "n.397T>G",
"hgvs_p": null,
"transcript": "ENST00000696106.1",
"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": 560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "C9",
"gene_hgnc_id": 1358,
"dbsnp": "rs121909593",
"frequency_reference_population": 0.00018897033,
"hom_count_reference_population": 0,
"allele_count_reference_population": 305,
"gnomad_exomes_af": 0.000194271,
"gnomad_genomes_af": 0.000138036,
"gnomad_exomes_ac": 284,
"gnomad_genomes_ac": 21,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9632248878479004,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.938,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9227,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.54,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.271,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000263408.5",
"gene_symbol": "C9",
"hgnc_id": 1358,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.355T>G",
"hgvs_p": "p.Cys119Gly"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000696106.1",
"gene_symbol": "ENSG00000289699",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.397T>G",
"hgvs_p": null
}
],
"clinvar_disease": "Age related macular degeneration 15,Complement component 9 deficiency,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:3",
"phenotype_combined": "Complement component 9 deficiency|Age related macular degeneration 15;Complement component 9 deficiency|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}