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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: 19-42248868-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=42248868&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 42248868,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000222329.9",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.1244C>T",
"hgvs_p": "p.Ala415Val",
"transcript": "NM_006494.4",
"protein_id": "NP_006485.2",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 548,
"cds_start": 1244,
"cds_end": null,
"cds_length": 1647,
"cdna_start": 1373,
"cdna_end": null,
"cdna_length": 2672,
"mane_select": "ENST00000222329.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.1244C>T",
"hgvs_p": "p.Ala415Val",
"transcript": "ENST00000222329.9",
"protein_id": "ENSP00000222329.3",
"transcript_support_level": 1,
"aa_start": 415,
"aa_end": null,
"aa_length": 548,
"cds_start": 1244,
"cds_end": null,
"cds_length": 1647,
"cdna_start": 1373,
"cdna_end": null,
"cdna_length": 2672,
"mane_select": "NM_006494.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000268643",
"gene_hgnc_id": null,
"hgvs_c": "c.22+6110C>T",
"hgvs_p": null,
"transcript": "ENST00000594664.1",
"protein_id": "ENSP00000470087.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 166,
"cds_start": -4,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 634,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val",
"transcript": "NM_001301035.2",
"protein_id": "NP_001287964.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 473,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1422,
"cdna_start": 1321,
"cdna_end": null,
"cdna_length": 2620,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val",
"transcript": "NM_001308402.2",
"protein_id": "NP_001295331.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 473,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1422,
"cdna_start": 1280,
"cdna_end": null,
"cdna_length": 2579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val",
"transcript": "NM_001312656.2",
"protein_id": "NP_001299585.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 473,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1422,
"cdna_start": 1247,
"cdna_end": null,
"cdna_length": 2546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val",
"transcript": "NM_001440420.1",
"protein_id": "NP_001427349.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 473,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1422,
"cdna_start": 1499,
"cdna_end": null,
"cdna_length": 2798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val",
"transcript": "ENST00000440177.6",
"protein_id": "ENSP00000388173.2",
"transcript_support_level": 2,
"aa_start": 340,
"aa_end": null,
"aa_length": 473,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1422,
"cdna_start": 1321,
"cdna_end": null,
"cdna_length": 2032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.437C>T",
"hgvs_p": "p.Ala146Val",
"transcript": "NM_001440421.1",
"protein_id": "NP_001427350.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 279,
"cds_start": 437,
"cds_end": null,
"cds_length": 840,
"cdna_start": 1138,
"cdna_end": null,
"cdna_length": 2437,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ala340Val",
"transcript": "XM_047438394.1",
"protein_id": "XP_047294350.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 473,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1422,
"cdna_start": 1551,
"cdna_end": null,
"cdna_length": 2850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"hgvs_c": "c.*433C>T",
"hgvs_p": null,
"transcript": "ENST00000715593.1",
"protein_id": "ENSP00000520487.1",
"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": 2437,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000268643",
"gene_hgnc_id": null,
"hgvs_c": "n.-249C>T",
"hgvs_p": null,
"transcript": "ENST00000676949.1",
"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": 218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ERF",
"gene_hgnc_id": 3444,
"dbsnp": "rs139842507",
"frequency_reference_population": 0.0173679,
"hom_count_reference_population": 276,
"allele_count_reference_population": 27914,
"gnomad_exomes_af": 0.0179605,
"gnomad_genomes_af": 0.0117025,
"gnomad_exomes_ac": 26133,
"gnomad_genomes_ac": 1781,
"gnomad_exomes_homalt": 263,
"gnomad_genomes_homalt": 13,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0027230679988861084,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.071,
"revel_prediction": "Benign",
"alphamissense_score": 0.0762,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.035,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000222329.9",
"gene_symbol": "ERF",
"hgnc_id": 3444,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1244C>T",
"hgvs_p": "p.Ala415Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000594664.1",
"gene_symbol": "ENSG00000268643",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.22+6110C>T",
"hgvs_p": null
}
],
"clinvar_disease": "TWIST1-related craniosynostosis,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "TWIST1-related craniosynostosis|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}