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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: 19-44949172-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=44949172&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 44949172,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000252490.7",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC2",
"gene_hgnc_id": 609,
"hgvs_c": "c.229A>C",
"hgvs_p": "p.Lys77Gln",
"transcript": "NM_000483.5",
"protein_id": "NP_000474.2",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 101,
"cds_start": 229,
"cds_end": null,
"cds_length": 306,
"cdna_start": 267,
"cdna_end": null,
"cdna_length": 660,
"mane_select": "ENST00000252490.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC2",
"gene_hgnc_id": 609,
"hgvs_c": "c.229A>C",
"hgvs_p": "p.Lys77Gln",
"transcript": "ENST00000252490.7",
"protein_id": "ENSP00000252490.5",
"transcript_support_level": 2,
"aa_start": 77,
"aa_end": null,
"aa_length": 101,
"cds_start": 229,
"cds_end": null,
"cds_length": 306,
"cdna_start": 267,
"cdna_end": null,
"cdna_length": 660,
"mane_select": "NM_000483.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC4-APOC2",
"gene_hgnc_id": 44426,
"hgvs_c": "c.460A>C",
"hgvs_p": "p.Lys154Gln",
"transcript": "ENST00000589057.5",
"protein_id": "ENSP00000468139.1",
"transcript_support_level": 5,
"aa_start": 154,
"aa_end": null,
"aa_length": 178,
"cds_start": 460,
"cds_end": null,
"cds_length": 537,
"cdna_start": 482,
"cdna_end": null,
"cdna_length": 680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC2",
"gene_hgnc_id": 609,
"hgvs_c": "c.229A>C",
"hgvs_p": "p.Lys77Gln",
"transcript": "ENST00000590360.2",
"protein_id": "ENSP00000466775.1",
"transcript_support_level": 3,
"aa_start": 77,
"aa_end": null,
"aa_length": 101,
"cds_start": 229,
"cds_end": null,
"cds_length": 306,
"cdna_start": 351,
"cdna_end": null,
"cdna_length": 744,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC2",
"gene_hgnc_id": 609,
"hgvs_c": "c.187A>C",
"hgvs_p": "p.Lys63Gln",
"transcript": "ENST00000591597.5",
"protein_id": "ENSP00000476835.1",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 87,
"cds_start": 187,
"cds_end": null,
"cds_length": 264,
"cdna_start": 220,
"cdna_end": null,
"cdna_length": 447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC4-APOC2",
"gene_hgnc_id": 44426,
"hgvs_c": "n.*1012A>C",
"hgvs_p": null,
"transcript": "ENST00000585685.5",
"protein_id": "ENSP00000467185.1",
"transcript_support_level": 5,
"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": 1829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC4-APOC2",
"gene_hgnc_id": 44426,
"hgvs_c": "n.1436A>C",
"hgvs_p": null,
"transcript": "NR_037932.1",
"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": 1829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC2",
"gene_hgnc_id": 609,
"hgvs_c": "c.*308A>C",
"hgvs_p": null,
"transcript": "ENST00000585786.1",
"protein_id": "ENSP00000465001.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 72,
"cds_start": -4,
"cds_end": null,
"cds_length": 219,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC2",
"gene_hgnc_id": 609,
"hgvs_c": "c.*23A>C",
"hgvs_p": null,
"transcript": "ENST00000592257.5",
"protein_id": "ENSP00000477261.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 47,
"cds_start": -4,
"cds_end": null,
"cds_length": 144,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOC4-APOC2",
"gene_hgnc_id": 44426,
"hgvs_c": "n.*1012A>C",
"hgvs_p": null,
"transcript": "ENST00000585685.5",
"protein_id": "ENSP00000467185.1",
"transcript_support_level": 5,
"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": 1829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "APOC2",
"gene_hgnc_id": 609,
"dbsnp": "rs5126",
"frequency_reference_population": 0.0013651382,
"hom_count_reference_population": 31,
"allele_count_reference_population": 2203,
"gnomad_exomes_af": 0.000755298,
"gnomad_genomes_af": 0.00722636,
"gnomad_exomes_ac": 1104,
"gnomad_genomes_ac": 1099,
"gnomad_exomes_homalt": 16,
"gnomad_genomes_homalt": 15,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0037645697593688965,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.337,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1407,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.076,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": "ENST00000252490.7",
"gene_symbol": "APOC2",
"hgnc_id": 609,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,SD",
"hgvs_c": "c.229A>C",
"hgvs_p": "p.Lys77Gln"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000589057.5",
"gene_symbol": "APOC4-APOC2",
"hgnc_id": 44426,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.460A>C",
"hgvs_p": "p.Lys154Gln"
}
],
"clinvar_disease": "APOLIPOPROTEIN C-II (AFRICAN),Cardiovascular phenotype,Familial apolipoprotein C-II deficiency,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:4",
"phenotype_combined": "APOLIPOPROTEIN C-II (AFRICAN)|not provided|Familial apolipoprotein C-II deficiency|Cardiovascular phenotype|not specified",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}