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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: 3-54891437-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=54891437&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 54891437,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_018398.3",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2233C>G",
"hgvs_p": "p.Gln745Glu",
"transcript": "NM_018398.3",
"protein_id": "NP_060868.2",
"transcript_support_level": null,
"aa_start": 745,
"aa_end": null,
"aa_length": 1091,
"cds_start": 2233,
"cds_end": null,
"cds_length": 3276,
"cdna_start": 2395,
"cdna_end": null,
"cdna_length": 3789,
"mane_select": "ENST00000474759.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018398.3"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2233C>G",
"hgvs_p": "p.Gln745Glu",
"transcript": "ENST00000474759.6",
"protein_id": "ENSP00000419101.1",
"transcript_support_level": 1,
"aa_start": 745,
"aa_end": null,
"aa_length": 1091,
"cds_start": 2233,
"cds_end": null,
"cds_length": 3276,
"cdna_start": 2395,
"cdna_end": null,
"cdna_length": 3789,
"mane_select": "NM_018398.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000474759.6"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.1951C>G",
"hgvs_p": "p.Gln651Glu",
"transcript": "ENST00000490478.5",
"protein_id": "ENSP00000417279.1",
"transcript_support_level": 1,
"aa_start": 651,
"aa_end": null,
"aa_length": 997,
"cds_start": 1951,
"cds_end": null,
"cds_length": 2994,
"cdna_start": 2163,
"cdna_end": null,
"cdna_length": 3557,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000490478.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "n.*311C>G",
"hgvs_p": null,
"transcript": "ENST00000471363.5",
"protein_id": "ENSP00000418228.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3477,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000471363.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "n.*311C>G",
"hgvs_p": null,
"transcript": "ENST00000471363.5",
"protein_id": "ENSP00000418228.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3477,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000471363.5"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2215C>G",
"hgvs_p": "p.Gln739Glu",
"transcript": "ENST00000958523.1",
"protein_id": "ENSP00000628582.1",
"transcript_support_level": null,
"aa_start": 739,
"aa_end": null,
"aa_length": 1085,
"cds_start": 2215,
"cds_end": null,
"cds_length": 3258,
"cdna_start": 2502,
"cdna_end": null,
"cdna_length": 3896,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958523.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2125C>G",
"hgvs_p": "p.Gln709Glu",
"transcript": "ENST00000958525.1",
"protein_id": "ENSP00000628584.1",
"transcript_support_level": null,
"aa_start": 709,
"aa_end": null,
"aa_length": 1055,
"cds_start": 2125,
"cds_end": null,
"cds_length": 3168,
"cdna_start": 2250,
"cdna_end": null,
"cdna_length": 3634,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958525.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2089C>G",
"hgvs_p": "p.Gln697Glu",
"transcript": "ENST00000958524.1",
"protein_id": "ENSP00000628583.1",
"transcript_support_level": null,
"aa_start": 697,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2089,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2238,
"cdna_end": null,
"cdna_length": 3630,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958524.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3-AS1",
"gene_hgnc_id": 40702,
"hgvs_c": "n.533+3176G>C",
"hgvs_p": null,
"transcript": "ENST00000471265.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2078,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000471265.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3-AS1",
"gene_hgnc_id": 40702,
"hgvs_c": "n.533+3176G>C",
"hgvs_p": null,
"transcript": "NR_046666.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2078,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_046666.1"
}
],
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"dbsnp": "rs751987684",
"frequency_reference_population": 0.0000027371725,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273717,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11027833819389343,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.157,
"revel_prediction": "Benign",
"alphamissense_score": 0.0693,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.006,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018398.3",
"gene_symbol": "CACNA2D3",
"hgnc_id": 15460,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2233C>G",
"hgvs_p": "p.Gln745Glu"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000471265.1",
"gene_symbol": "CACNA2D3-AS1",
"hgnc_id": 40702,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.533+3176G>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}