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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: 8-99778921-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=99778921&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 99778921,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000357162.7",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "c.7744G>A",
"hgvs_p": "p.Asp2582Asn",
"transcript": "NM_017890.5",
"protein_id": "NP_060360.3",
"transcript_support_level": null,
"aa_start": 2582,
"aa_end": null,
"aa_length": 4022,
"cds_start": 7744,
"cds_end": null,
"cds_length": 12069,
"cdna_start": 7847,
"cdna_end": null,
"cdna_length": 14086,
"mane_select": null,
"mane_plus": "ENST00000358544.7",
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "c.7744G>A",
"hgvs_p": "p.Asp2582Asn",
"transcript": "ENST00000358544.7",
"protein_id": "ENSP00000351346.2",
"transcript_support_level": 1,
"aa_start": 2582,
"aa_end": null,
"aa_length": 4022,
"cds_start": 7744,
"cds_end": null,
"cds_length": 12069,
"cdna_start": 7847,
"cdna_end": null,
"cdna_length": 14086,
"mane_select": null,
"mane_plus": "NM_017890.5",
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "c.7669G>A",
"hgvs_p": "p.Asp2557Asn",
"transcript": "NM_152564.5",
"protein_id": "NP_689777.3",
"transcript_support_level": null,
"aa_start": 2557,
"aa_end": null,
"aa_length": 3997,
"cds_start": 7669,
"cds_end": null,
"cds_length": 11994,
"cdna_start": 7772,
"cdna_end": null,
"cdna_length": 14011,
"mane_select": "ENST00000357162.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "c.7669G>A",
"hgvs_p": "p.Asp2557Asn",
"transcript": "ENST00000357162.7",
"protein_id": "ENSP00000349685.2",
"transcript_support_level": 1,
"aa_start": 2557,
"aa_end": null,
"aa_length": 3997,
"cds_start": 7669,
"cds_end": null,
"cds_length": 11994,
"cdna_start": 7772,
"cdna_end": null,
"cdna_length": 14011,
"mane_select": "NM_152564.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.7744G>A",
"hgvs_p": null,
"transcript": "ENST00000682153.1",
"protein_id": "ENSP00000507923.1",
"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": 14705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.7814G>A",
"hgvs_p": null,
"transcript": "ENST00000682358.1",
"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": 14588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.*3426G>A",
"hgvs_p": null,
"transcript": "ENST00000683334.1",
"protein_id": "ENSP00000507369.1",
"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": 13930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.*3426G>A",
"hgvs_p": null,
"transcript": "ENST00000683334.1",
"protein_id": "ENSP00000507369.1",
"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": 13930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"hgvs_c": "n.*86G>A",
"hgvs_p": null,
"transcript": "ENST00000518569.1",
"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": 531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VPS13B",
"gene_hgnc_id": 2183,
"dbsnp": "rs773242093",
"frequency_reference_population": 0.00022431667,
"hom_count_reference_population": 0,
"allele_count_reference_population": 362,
"gnomad_exomes_af": 0.00021756,
"gnomad_genomes_af": 0.000289234,
"gnomad_exomes_ac": 318,
"gnomad_genomes_ac": 44,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.025090008974075317,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.058,
"revel_prediction": "Benign",
"alphamissense_score": 0.0646,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.65,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.618,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000357162.7",
"gene_symbol": "VPS13B",
"hgnc_id": 2183,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7669G>A",
"hgvs_p": "p.Asp2557Asn"
}
],
"clinvar_disease": "Cohen syndrome,Inborn genetic diseases,VPS13B-related disorder,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 LB:1 B:1",
"phenotype_combined": "Cohen syndrome|not provided|Inborn genetic diseases|VPS13B-related disorder|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}