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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: X-15764682-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=15764682&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CA5B",
"hgnc_id": 1378,
"hgvs_c": "c.247C>G",
"hgvs_p": "p.Leu83Val",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_007220.4",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BS2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "CA5BP1-CA5B",
"hgnc_id": null,
"hgvs_c": "n.1011C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "NR_160544.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_score": -4,
"allele_count_reference_population": 14,
"alphamissense_prediction": null,
"alphamissense_score": 0.1917,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.27,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.7183019518852234,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 317,
"aa_ref": "L",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6837,
"cdna_start": 383,
"cds_end": null,
"cds_length": 954,
"cds_start": 247,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_007220.4",
"gene_hgnc_id": 1378,
"gene_symbol": "CA5B",
"hgvs_c": "c.247C>G",
"hgvs_p": "p.Leu83Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000318636.8",
"protein_coding": true,
"protein_id": "NP_009151.1",
"strand": true,
"transcript": "NM_007220.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 317,
"aa_ref": "L",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6837,
"cdna_start": 383,
"cds_end": null,
"cds_length": 954,
"cds_start": 247,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000318636.8",
"gene_hgnc_id": 1378,
"gene_symbol": "CA5B",
"hgvs_c": "c.247C>G",
"hgvs_p": "p.Leu83Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007220.4",
"protein_coding": true,
"protein_id": "ENSP00000314099.3",
"strand": true,
"transcript": "ENST00000318636.8",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 332,
"aa_ref": "L",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1963,
"cdna_start": 380,
"cds_end": null,
"cds_length": 999,
"cds_start": 247,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000948118.1",
"gene_hgnc_id": 1378,
"gene_symbol": "CA5B",
"hgvs_c": "c.247C>G",
"hgvs_p": "p.Leu83Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618177.1",
"strand": true,
"transcript": "ENST00000948118.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 135,
"aa_ref": "L",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 529,
"cdna_start": 368,
"cds_end": null,
"cds_length": 408,
"cds_start": 247,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000479740.5",
"gene_hgnc_id": 1378,
"gene_symbol": "CA5B",
"hgvs_c": "c.247C>G",
"hgvs_p": "p.Leu83Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000417553.1",
"strand": true,
"transcript": "ENST00000479740.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 652,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000380319.2",
"gene_hgnc_id": 1378,
"gene_symbol": "CA5B",
"hgvs_c": "n.423C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000380319.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 517,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000478341.1",
"gene_hgnc_id": 1378,
"gene_symbol": "CA5B",
"hgvs_c": "n.85C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000417236.1",
"strand": true,
"transcript": "ENST00000478341.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 8116,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NR_160544.1",
"gene_hgnc_id": null,
"gene_symbol": "CA5BP1-CA5B",
"hgvs_c": "n.1011C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_160544.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2507,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NR_160545.1",
"gene_hgnc_id": null,
"gene_symbol": "CA5BP1-CA5B",
"hgvs_c": "n.1011C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_160545.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 75,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 488,
"cdna_start": null,
"cds_end": null,
"cds_length": 230,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000498004.5",
"gene_hgnc_id": 1378,
"gene_symbol": "CA5B",
"hgvs_c": "c.*17C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418622.1",
"strand": true,
"transcript": "ENST00000498004.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1379030882",
"effect": "missense_variant",
"frequency_reference_population": 0.000011700804,
"gene_hgnc_id": 1378,
"gene_symbol": "CA5B",
"gnomad_exomes_ac": 13,
"gnomad_exomes_af": 0.0000119565,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000915575,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 3,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.345,
"pos": 15764682,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.509,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_007220.4"
}
]
}