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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: 12-54028780-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=54028780&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 54028780,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004503.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.259T>C",
"hgvs_p": "p.Cys87Arg",
"transcript": "NM_004503.4",
"protein_id": "NP_004494.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 235,
"cds_start": 259,
"cds_end": null,
"cds_length": 708,
"cdna_start": 341,
"cdna_end": null,
"cdna_length": 1651,
"mane_select": "ENST00000243108.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.259T>C",
"hgvs_p": "p.Cys87Arg",
"transcript": "ENST00000243108.5",
"protein_id": "ENSP00000243108.4",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 235,
"cds_start": 259,
"cds_end": null,
"cds_length": 708,
"cdna_start": 341,
"cdna_end": null,
"cdna_length": 1651,
"mane_select": "NM_004503.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.13T>C",
"hgvs_p": "p.Cys5Arg",
"transcript": "ENST00000394331.3",
"protein_id": "ENSP00000377864.3",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 153,
"cds_start": 13,
"cds_end": null,
"cds_length": 462,
"cdna_start": 1723,
"cdna_end": null,
"cdna_length": 2943,
"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+11366T>C",
"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": 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.167-5498T>C",
"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.306-5498T>C",
"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": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.13T>C",
"hgvs_p": "p.Cys5Arg",
"transcript": "NM_153693.5",
"protein_id": "NP_710160.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 153,
"cds_start": 13,
"cds_end": null,
"cds_length": 462,
"cdna_start": 732,
"cdna_end": null,
"cdna_length": 2042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.13T>C",
"hgvs_p": "p.Cys5Arg",
"transcript": "ENST00000509328.1",
"protein_id": "ENSP00000423898.1",
"transcript_support_level": 3,
"aa_start": 5,
"aa_end": null,
"aa_length": 70,
"cds_start": 13,
"cds_end": null,
"cds_length": 213,
"cdna_start": 158,
"cdna_end": null,
"cdna_length": 358,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.13T>C",
"hgvs_p": "p.Cys5Arg",
"transcript": "ENST00000504315.1",
"protein_id": "ENSP00000424124.1",
"transcript_support_level": 3,
"aa_start": 5,
"aa_end": null,
"aa_length": 50,
"cds_start": 13,
"cds_end": null,
"cds_length": 155,
"cdna_start": 396,
"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": 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+11366T>C",
"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": 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.528-5498T>C",
"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": "HOXC6",
"gene_hgnc_id": 5128,
"dbsnp": "rs532429929",
"frequency_reference_population": 0.0000018585426,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000136809,
"gnomad_genomes_af": 0.00000656711,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5665806531906128,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.605,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7532,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.209,
"phylop100way_prediction": "Benign",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004503.4",
"gene_symbol": "HOXC6",
"hgnc_id": 5128,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.259T>C",
"hgvs_p": "p.Cys87Arg"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000513209.1",
"gene_symbol": "ENSG00000273049",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.167-5498T>C",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_014620.6",
"gene_symbol": "HOXC4",
"hgnc_id": 5126,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-124+11366T>C",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000512206.1",
"gene_symbol": "ENSG00000273046",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.306-5498T>C",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NR_003084.3",
"gene_symbol": "HOXC5",
"hgnc_id": 5127,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.528-5498T>C",
"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
}