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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: 1-11846011-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=11846011&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 11846011,
"ref": "A",
"alt": "G",
"effect": "stop_lost",
"transcript": "ENST00000376480.7",
"consequences": [
{
"aa_ref": "*",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPPA",
"gene_hgnc_id": 7939,
"hgvs_c": "c.454T>C",
"hgvs_p": "p.Ter152Argext*?",
"transcript": "NM_006172.4",
"protein_id": "NP_006163.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 151,
"cds_start": 454,
"cds_end": null,
"cds_length": 456,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 855,
"mane_select": "ENST00000376480.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPPA",
"gene_hgnc_id": 7939,
"hgvs_c": "c.454T>C",
"hgvs_p": "p.Ter152Argext*?",
"transcript": "ENST00000376480.7",
"protein_id": "ENSP00000365663.3",
"transcript_support_level": 1,
"aa_start": 152,
"aa_end": null,
"aa_length": 151,
"cds_start": 454,
"cds_end": null,
"cds_length": 456,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 855,
"mane_select": "NM_006172.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CLCN6",
"gene_hgnc_id": 2024,
"hgvs_c": "n.781+245A>G",
"hgvs_p": null,
"transcript": "ENST00000446542.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPPA",
"gene_hgnc_id": 7939,
"hgvs_c": "c.304T>C",
"hgvs_p": "p.Ter102Argext*?",
"transcript": "ENST00000376476.1",
"protein_id": "ENSP00000365659.1",
"transcript_support_level": 3,
"aa_start": 102,
"aa_end": null,
"aa_length": 101,
"cds_start": 304,
"cds_end": null,
"cds_length": 306,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 728,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "CLCN6",
"gene_hgnc_id": 2024,
"hgvs_c": "n.*1961+245A>G",
"hgvs_p": null,
"transcript": "ENST00000400892.3",
"protein_id": "ENSP00000496938.1",
"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": 3993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NPPA-AS1",
"gene_hgnc_id": 37635,
"hgvs_c": "n.1479+245A>G",
"hgvs_p": null,
"transcript": "NR_037806.1",
"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": 1662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPPA",
"gene_hgnc_id": 7939,
"dbsnp": "rs5065",
"frequency_reference_population": 0.15262234,
"hom_count_reference_population": 22231,
"allele_count_reference_population": 246218,
"gnomad_exomes_af": 0.147,
"gnomad_genomes_af": 0.20664,
"gnomad_exomes_ac": 214793,
"gnomad_genomes_ac": 31425,
"gnomad_exomes_homalt": 17759,
"gnomad_genomes_homalt": 4472,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.46000000834465027,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.328,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "PM4,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 16,
"pathogenic_score": 2,
"criteria": [
"PM4",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000376480.7",
"gene_symbol": "NPPA",
"hgnc_id": 7939,
"effects": [
"stop_lost"
],
"inheritance_mode": "AD,Unknown,AR",
"hgvs_c": "c.454T>C",
"hgvs_p": "p.Ter152Argext*?"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000446542.5",
"gene_symbol": "CLCN6",
"hgnc_id": 2024,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.781+245A>G",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NR_037806.1",
"gene_symbol": "NPPA-AS1",
"hgnc_id": 37635,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1479+245A>G",
"hgvs_p": null
}
],
"clinvar_disease": " 6, familial,Atrial fibrillation,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|not provided|Atrial fibrillation, familial, 6",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}