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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: 9-98542020-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=98542020&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 98542020,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000259455.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.483T>C",
"hgvs_p": "p.Pro161Pro",
"transcript": "NM_005458.8",
"protein_id": "NP_005449.5",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 941,
"cds_start": 483,
"cds_end": null,
"cds_length": 2826,
"cdna_start": 681,
"cdna_end": null,
"cdna_length": 5499,
"mane_select": "ENST00000259455.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.483T>C",
"hgvs_p": "p.Pro161Pro",
"transcript": "ENST00000259455.4",
"protein_id": "ENSP00000259455.2",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 941,
"cds_start": 483,
"cds_end": null,
"cds_length": 2826,
"cdna_start": 681,
"cdna_end": null,
"cdna_length": 5499,
"mane_select": "NM_005458.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.99T>C",
"hgvs_p": "p.Pro33Pro",
"transcript": "ENST00000637717.1",
"protein_id": "ENSP00000490789.1",
"transcript_support_level": 5,
"aa_start": 33,
"aa_end": null,
"aa_length": 76,
"cds_start": 99,
"cds_end": null,
"cds_length": 232,
"cdna_start": 380,
"cdna_end": null,
"cdna_length": 513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "c.189T>C",
"hgvs_p": "p.Pro63Pro",
"transcript": "XM_017015331.3",
"protein_id": "XP_016870820.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 843,
"cds_start": 189,
"cds_end": null,
"cds_length": 2532,
"cdna_start": 360,
"cdna_end": null,
"cdna_length": 5178,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "n.270T>C",
"hgvs_p": null,
"transcript": "ENST00000477471.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "n.257T>C",
"hgvs_p": null,
"transcript": "ENST00000634227.1",
"protein_id": null,
"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": 583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "n.261T>C",
"hgvs_p": null,
"transcript": "ENST00000637410.1",
"protein_id": null,
"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": 2541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"hgvs_c": "n.93T>C",
"hgvs_p": null,
"transcript": "ENST00000638001.1",
"protein_id": null,
"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": 100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GABBR2",
"gene_hgnc_id": 4507,
"dbsnp": "rs35449008",
"frequency_reference_population": 0.036836483,
"hom_count_reference_population": 1772,
"allele_count_reference_population": 59456,
"gnomad_exomes_af": 0.0338419,
"gnomad_genomes_af": 0.0655751,
"gnomad_exomes_ac": 49468,
"gnomad_genomes_ac": 9988,
"gnomad_exomes_homalt": 1211,
"gnomad_genomes_homalt": 561,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6499999761581421,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.65,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.664,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000259455.4",
"gene_symbol": "GABBR2",
"hgnc_id": 4507,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.483T>C",
"hgvs_p": "p.Pro161Pro"
}
],
"clinvar_disease": "Epileptic encephalopathy,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Epileptic encephalopathy|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}