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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: 4-125451820-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=125451820&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 125451820,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000394329.9",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.10810A>C",
"hgvs_p": "p.Ile3604Leu",
"transcript": "NM_001291303.3",
"protein_id": "NP_001278232.1",
"transcript_support_level": null,
"aa_start": 3604,
"aa_end": null,
"aa_length": 4983,
"cds_start": 10810,
"cds_end": null,
"cds_length": 14952,
"cdna_start": 11845,
"cdna_end": null,
"cdna_length": 17151,
"mane_select": "ENST00000394329.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.10810A>C",
"hgvs_p": "p.Ile3604Leu",
"transcript": "ENST00000394329.9",
"protein_id": "ENSP00000377862.4",
"transcript_support_level": 5,
"aa_start": 3604,
"aa_end": null,
"aa_length": 4983,
"cds_start": 10810,
"cds_end": null,
"cds_length": 14952,
"cdna_start": 11845,
"cdna_end": null,
"cdna_length": 17151,
"mane_select": "NM_001291303.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.5698A>C",
"hgvs_p": "p.Ile1900Leu",
"transcript": "ENST00000335110.5",
"protein_id": "ENSP00000335169.5",
"transcript_support_level": 1,
"aa_start": 1900,
"aa_end": null,
"aa_length": 3222,
"cds_start": 5698,
"cds_end": null,
"cds_length": 9669,
"cdna_start": 5698,
"cdna_end": null,
"cdna_length": 9669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.10810A>C",
"hgvs_p": "p.Ile3604Leu",
"transcript": "NM_001438396.1",
"protein_id": "NP_001425325.1",
"transcript_support_level": null,
"aa_start": 3604,
"aa_end": null,
"aa_length": 4983,
"cds_start": 10810,
"cds_end": null,
"cds_length": 14952,
"cdna_start": 12267,
"cdna_end": null,
"cdna_length": 17573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.10810A>C",
"hgvs_p": "p.Ile3604Leu",
"transcript": "NM_001291285.3",
"protein_id": "NP_001278214.1",
"transcript_support_level": null,
"aa_start": 3604,
"aa_end": null,
"aa_length": 4982,
"cds_start": 10810,
"cds_end": null,
"cds_length": 14949,
"cdna_start": 11845,
"cdna_end": null,
"cdna_length": 17148,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.10810A>C",
"hgvs_p": "p.Ile3604Leu",
"transcript": "NM_001438397.1",
"protein_id": "NP_001425326.1",
"transcript_support_level": null,
"aa_start": 3604,
"aa_end": null,
"aa_length": 4982,
"cds_start": 10810,
"cds_end": null,
"cds_length": 14949,
"cdna_start": 12267,
"cdna_end": null,
"cdna_length": 17570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.10804A>C",
"hgvs_p": "p.Ile3602Leu",
"transcript": "NM_024582.6",
"protein_id": "NP_078858.4",
"transcript_support_level": null,
"aa_start": 3602,
"aa_end": null,
"aa_length": 4981,
"cds_start": 10804,
"cds_end": null,
"cds_length": 14946,
"cdna_start": 11839,
"cdna_end": null,
"cdna_length": 17145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.5581A>C",
"hgvs_p": "p.Ile1861Leu",
"transcript": "NM_001437895.1",
"protein_id": "NP_001424824.1",
"transcript_support_level": null,
"aa_start": 1861,
"aa_end": null,
"aa_length": 3240,
"cds_start": 5581,
"cds_end": null,
"cds_length": 9723,
"cdna_start": 6658,
"cdna_end": null,
"cdna_length": 11964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.5581A>C",
"hgvs_p": "p.Ile1861Leu",
"transcript": "ENST00000674496.2",
"protein_id": "ENSP00000501473.2",
"transcript_support_level": null,
"aa_start": 1861,
"aa_end": null,
"aa_length": 3240,
"cds_start": 5581,
"cds_end": null,
"cds_length": 9723,
"cdna_start": 6695,
"cdna_end": null,
"cdna_length": 12001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"dbsnp": "rs76491994",
"frequency_reference_population": 0.013837727,
"hom_count_reference_population": 221,
"allele_count_reference_population": 22336,
"gnomad_exomes_af": 0.0142381,
"gnomad_genomes_af": 0.00999422,
"gnomad_exomes_ac": 20814,
"gnomad_genomes_ac": 1522,
"gnomad_exomes_homalt": 205,
"gnomad_genomes_homalt": 16,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0034600794315338135,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.064,
"revel_prediction": "Benign",
"alphamissense_score": 0.2611,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.972,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000394329.9",
"gene_symbol": "FAT4",
"hgnc_id": 23109,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.10810A>C",
"hgvs_p": "p.Ile3604Leu"
}
],
"clinvar_disease": "Hennekam lymphangiectasia-lymphedema syndrome 2,Van Maldergem syndrome 2,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:4",
"phenotype_combined": "not provided|not specified|Hennekam lymphangiectasia-lymphedema syndrome 2;Van Maldergem syndrome 2",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}