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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: 5-77063199-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=77063199&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "AGGF1",
"hgnc_id": 24684,
"hgvs_c": "c.2092C>A",
"hgvs_p": "p.Pro698Thr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_018046.5",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000285000",
"hgnc_id": null,
"hgvs_c": "n.1809+1397C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000646704.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 434663,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.061,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.72,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.002901822328567505,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 714,
"aa_ref": "P",
"aa_start": 698,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4490,
"cdna_start": 2455,
"cds_end": null,
"cds_length": 2145,
"cds_start": 2092,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_018046.5",
"gene_hgnc_id": 24684,
"gene_symbol": "AGGF1",
"hgvs_c": "c.2092C>A",
"hgvs_p": "p.Pro698Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000312916.12",
"protein_coding": true,
"protein_id": "NP_060516.2",
"strand": true,
"transcript": "NM_018046.5",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 714,
"aa_ref": "P",
"aa_start": 698,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4490,
"cdna_start": 2455,
"cds_end": null,
"cds_length": 2145,
"cds_start": 2092,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000312916.12",
"gene_hgnc_id": 24684,
"gene_symbol": "AGGF1",
"hgvs_c": "c.2092C>A",
"hgvs_p": "p.Pro698Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018046.5",
"protein_coding": true,
"protein_id": "ENSP00000316109.7",
"strand": true,
"transcript": "ENST00000312916.12",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 2348,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000646704.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285000",
"hgvs_c": "n.1809+1397C>A",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000495089.1",
"strand": true,
"transcript": "ENST00000646704.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 713,
"aa_ref": "P",
"aa_start": 697,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2911,
"cdna_start": 2458,
"cds_end": null,
"cds_length": 2142,
"cds_start": 2089,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000949072.1",
"gene_hgnc_id": 24684,
"gene_symbol": "AGGF1",
"hgvs_c": "c.2089C>A",
"hgvs_p": "p.Pro697Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619131.1",
"strand": true,
"transcript": "ENST00000949072.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 709,
"aa_ref": "P",
"aa_start": 693,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4435,
"cdna_start": 2439,
"cds_end": null,
"cds_length": 2130,
"cds_start": 2077,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000920273.1",
"gene_hgnc_id": 24684,
"gene_symbol": "AGGF1",
"hgvs_c": "c.2077C>A",
"hgvs_p": "p.Pro693Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590332.1",
"strand": true,
"transcript": "ENST00000920273.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 686,
"aa_ref": "P",
"aa_start": 670,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4385,
"cdna_start": 2371,
"cds_end": null,
"cds_length": 2061,
"cds_start": 2008,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000871352.1",
"gene_hgnc_id": 24684,
"gene_symbol": "AGGF1",
"hgvs_c": "c.2008C>A",
"hgvs_p": "p.Pro670Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541411.1",
"strand": true,
"transcript": "ENST00000871352.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 651,
"aa_ref": "P",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2741,
"cdna_start": 2266,
"cds_end": null,
"cds_length": 1956,
"cds_start": 1903,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000871353.1",
"gene_hgnc_id": 24684,
"gene_symbol": "AGGF1",
"hgvs_c": "c.1903C>A",
"hgvs_p": "p.Pro635Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541412.1",
"strand": true,
"transcript": "ENST00000871353.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 646,
"aa_ref": "P",
"aa_start": 630,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4269,
"cdna_start": 2268,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1888,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000920272.1",
"gene_hgnc_id": 24684,
"gene_symbol": "AGGF1",
"hgvs_c": "c.1888C>A",
"hgvs_p": "p.Pro630Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590331.1",
"strand": true,
"transcript": "ENST00000920272.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs34400049",
"effect": "missense_variant",
"frequency_reference_population": 0.26940742,
"gene_hgnc_id": 24684,
"gene_symbol": "AGGF1",
"gnomad_exomes_ac": 400174,
"gnomad_exomes_af": 0.273805,
"gnomad_exomes_homalt": 56660,
"gnomad_genomes_ac": 34489,
"gnomad_genomes_af": 0.227087,
"gnomad_genomes_homalt": 4484,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 61144,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.02,
"pos": 77063199,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.045,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_018046.5"
}
]
}