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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: 12-54023792-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=54023792&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 54023792,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000513209.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXC4",
"gene_hgnc_id": 5126,
"hgvs_c": "c.-124+6378C>T",
"hgvs_p": null,
"transcript": "ENST00000303406.4",
"protein_id": "ENSP00000305973.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 264,
"cds_start": -4,
"cds_end": null,
"cds_length": 795,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1524,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.-192-4784C>T",
"hgvs_p": null,
"transcript": "ENST00000394331.3",
"protein_id": "ENSP00000377864.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": -4,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2943,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000273049",
"gene_hgnc_id": null,
"hgvs_c": "c.167-10486C>T",
"hgvs_p": null,
"transcript": "ENST00000513209.1",
"protein_id": "ENSP00000476742.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 126,
"cds_start": -4,
"cds_end": null,
"cds_length": 381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 777,
"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": "ENSG00000273046",
"gene_hgnc_id": null,
"hgvs_c": "n.305+6378C>T",
"hgvs_p": null,
"transcript": "ENST00000512206.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 1389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXC4",
"gene_hgnc_id": 5126,
"hgvs_c": "c.-124+6378C>T",
"hgvs_p": null,
"transcript": "NM_014620.6",
"protein_id": "NP_055435.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 264,
"cds_start": -4,
"cds_end": null,
"cds_length": 795,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2270,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.-192-4784C>T",
"hgvs_p": null,
"transcript": "NM_153693.5",
"protein_id": "NP_710160.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": -4,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.-72-4904C>T",
"hgvs_p": null,
"transcript": "ENST00000509328.1",
"protein_id": "ENSP00000423898.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 70,
"cds_start": -4,
"cds_end": null,
"cds_length": 213,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 358,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.-192-4784C>T",
"hgvs_p": null,
"transcript": "ENST00000504315.1",
"protein_id": "ENSP00000424124.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 50,
"cds_start": -4,
"cds_end": null,
"cds_length": 155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 538,
"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": "HOXC5",
"gene_hgnc_id": 5127,
"hgvs_c": "n.527+6378C>T",
"hgvs_p": null,
"transcript": "NR_003084.3",
"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": 1611,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ENSG00000273049",
"gene_hgnc_id": null,
"dbsnp": "rs736825",
"frequency_reference_population": 0.000026333113,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000263331,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7799999713897705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.105,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000513209.1",
"gene_symbol": "ENSG00000273049",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.167-10486C>T",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_014620.6",
"gene_symbol": "HOXC4",
"hgnc_id": 5126,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-124+6378C>T",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_153693.5",
"gene_symbol": "HOXC6",
"hgnc_id": 5128,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-192-4784C>T",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000512206.1",
"gene_symbol": "ENSG00000273046",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.305+6378C>T",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NR_003084.3",
"gene_symbol": "HOXC5",
"hgnc_id": 5127,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.527+6378C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}