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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: 2-130597896-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=130597896&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 130597896,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000259216.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFC1",
"gene_hgnc_id": 18292,
"hgvs_c": "c.334C>T",
"hgvs_p": "p.Arg112Cys",
"transcript": "NM_032545.4",
"protein_id": "NP_115934.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 223,
"cds_start": 334,
"cds_end": null,
"cds_length": 672,
"cdna_start": 622,
"cdna_end": null,
"cdna_length": 1672,
"mane_select": "ENST00000259216.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFC1",
"gene_hgnc_id": 18292,
"hgvs_c": "c.334C>T",
"hgvs_p": "p.Arg112Cys",
"transcript": "ENST00000259216.6",
"protein_id": "ENSP00000259216.5",
"transcript_support_level": 1,
"aa_start": 112,
"aa_end": null,
"aa_length": 223,
"cds_start": 334,
"cds_end": null,
"cds_length": 672,
"cdna_start": 622,
"cdna_end": null,
"cdna_length": 1672,
"mane_select": "NM_032545.4",
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CFC1",
"gene_hgnc_id": 18292,
"hgvs_c": "c.248-293C>T",
"hgvs_p": null,
"transcript": "NM_001270420.2",
"protein_id": "NP_001257349.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 191,
"cds_start": -4,
"cds_end": null,
"cds_length": 576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1557,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CFC1",
"gene_hgnc_id": 18292,
"hgvs_c": "c.248-293C>T",
"hgvs_p": null,
"transcript": "ENST00000615342.4",
"protein_id": "ENSP00000480526.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 191,
"cds_start": -4,
"cds_end": null,
"cds_length": 576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1554,
"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": "CFC1",
"gene_hgnc_id": 18292,
"hgvs_c": "c.247+746C>T",
"hgvs_p": null,
"transcript": "NM_001270421.2",
"protein_id": "NP_001257350.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 148,
"cds_start": -4,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1447,
"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": "CFC1",
"gene_hgnc_id": 18292,
"hgvs_c": "c.247+746C>T",
"hgvs_p": null,
"transcript": "ENST00000621673.4",
"protein_id": "ENSP00000480843.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 148,
"cds_start": -4,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1444,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000296255",
"gene_hgnc_id": null,
"hgvs_c": "n.271+436G>A",
"hgvs_p": null,
"transcript": "ENST00000737651.1",
"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": 616,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000296255",
"gene_hgnc_id": null,
"hgvs_c": "n.221+479G>A",
"hgvs_p": null,
"transcript": "ENST00000737652.1",
"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": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CFC1",
"gene_hgnc_id": 18292,
"hgvs_c": "c.*320C>T",
"hgvs_p": null,
"transcript": "XM_011511486.4",
"protein_id": "XP_011509788.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 142,
"cds_start": -4,
"cds_end": null,
"cds_length": 429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 935,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CFC1",
"gene_hgnc_id": 18292,
"dbsnp": "rs104893611",
"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": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9709912538528442,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.855,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.903,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.75,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": "ENST00000259216.6",
"gene_symbol": "CFC1",
"hgnc_id": 18292,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.334C>T",
"hgvs_p": "p.Arg112Cys"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000737651.1",
"gene_symbol": "ENSG00000296255",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.271+436G>A",
"hgvs_p": null
}
],
"clinvar_disease": " 2, autosomal, visceral,Heterotaxy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Heterotaxy, visceral, 2, autosomal",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}