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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: 20-63350730-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=63350730&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 11,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "CHRNA4",
"hgnc_id": 1958,
"hgvs_c": "c.681C>T",
"hgvs_p": "p.Ala227Ala",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -11,
"transcript": "NM_000744.7",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7,BS2",
"acmg_score": -11,
"allele_count_reference_population": 52,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.7,
"chr": "20",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Autosomal dominant nocturnal frontal lobe epilepsy",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.699999988079071,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 627,
"aa_ref": "A",
"aa_start": 227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5583,
"cdna_start": 865,
"cds_end": null,
"cds_length": 1884,
"cds_start": 681,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_000744.7",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "c.681C>T",
"hgvs_p": "p.Ala227Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000370263.9",
"protein_coding": true,
"protein_id": "NP_000735.1",
"strand": false,
"transcript": "NM_000744.7",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 627,
"aa_ref": "A",
"aa_start": 227,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5583,
"cdna_start": 865,
"cds_end": null,
"cds_length": 1884,
"cds_start": 681,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000370263.9",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "c.681C>T",
"hgvs_p": "p.Ala227Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000744.7",
"protein_coding": true,
"protein_id": "ENSP00000359285.4",
"strand": false,
"transcript": "ENST00000370263.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5201,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000463705.5",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.1329C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000463705.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2098,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000467563.3",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.751C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000467563.3",
"transcript_support_level": 1
},
{
"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": 2192,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000627000.1",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.*370C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000486914.1",
"strand": false,
"transcript": "ENST00000627000.1",
"transcript_support_level": 1
},
{
"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": 2192,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000627000.1",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.*370C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000486914.1",
"strand": false,
"transcript": "ENST00000627000.1",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 451,
"aa_ref": "A",
"aa_start": 51,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5514,
"cdna_start": 796,
"cds_end": null,
"cds_length": 1356,
"cds_start": 153,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001256573.2",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "c.153C>T",
"hgvs_p": "p.Ala51Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001243502.1",
"strand": false,
"transcript": "NM_001256573.2",
"transcript_support_level": null
},
{
"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": 2052,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000498043.6",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.*292C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000429513.1",
"strand": false,
"transcript": "ENST00000498043.6",
"transcript_support_level": 5
},
{
"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": 1603,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000630240.1",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.402C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000630240.1",
"transcript_support_level": 6
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5608,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NR_046317.2",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.890C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_046317.2",
"transcript_support_level": null
},
{
"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": 2052,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000498043.6",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.*292C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000429513.1",
"strand": false,
"transcript": "ENST00000498043.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 546,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000628665.1",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.*178C>T",
"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": "ENST00000628665.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 85,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000637243.1",
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"hgvs_c": "n.*247C>T",
"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": "ENST00000637243.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs45588436",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000032228276,
"gene_hgnc_id": 1958,
"gene_symbol": "CHRNA4",
"gnomad_exomes_ac": 50,
"gnomad_exomes_af": 0.0000342071,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131747,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "Autosomal dominant nocturnal frontal lobe epilepsy",
"phylop100way_prediction": "Benign",
"phylop100way_score": -2.314,
"pos": 63350730,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000744.7"
}
]
}