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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: 4-56017835-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=56017835&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "CEP135",
"hgnc_id": 29086,
"hgvs_c": "c.2990C>A",
"hgvs_p": "p.Ser997*",
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_025009.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.62,
"chr": "4",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": " autosomal recessive, primary,Microcephaly 8,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6200000047683716,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1140,
"aa_ref": "S",
"aa_start": 997,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5596,
"cdna_start": 3150,
"cds_end": null,
"cds_length": 3423,
"cds_start": 2990,
"consequences": [
"stop_gained"
],
"exon_count": 26,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "NM_025009.5",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.2990C>A",
"hgvs_p": "p.Ser997*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000257287.5",
"protein_coding": true,
"protein_id": "NP_079285.2",
"strand": true,
"transcript": "NM_025009.5",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1140,
"aa_ref": "S",
"aa_start": 997,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5596,
"cdna_start": 3150,
"cds_end": null,
"cds_length": 3423,
"cds_start": 2990,
"consequences": [
"stop_gained"
],
"exon_count": 26,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000257287.5",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.2990C>A",
"hgvs_p": "p.Ser997*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_025009.5",
"protein_coding": true,
"protein_id": "ENSP00000257287.3",
"strand": true,
"transcript": "ENST00000257287.5",
"transcript_support_level": 1
},
{
"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": 5129,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000506202.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "n.2940C>A",
"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": "ENST00000506202.1",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1191,
"aa_ref": "S",
"aa_start": 1048,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5781,
"cdna_start": 3335,
"cds_end": null,
"cds_length": 3576,
"cds_start": 3143,
"consequences": [
"stop_gained"
],
"exon_count": 27,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000916105.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.3143C>A",
"hgvs_p": "p.Ser1048*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586164.1",
"strand": true,
"transcript": "ENST00000916105.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1129,
"aa_ref": "S",
"aa_start": 986,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5651,
"cdna_start": 3210,
"cds_end": null,
"cds_length": 3390,
"cds_start": 2957,
"consequences": [
"stop_gained"
],
"exon_count": 26,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000916104.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.2957C>A",
"hgvs_p": "p.Ser986*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586163.1",
"strand": true,
"transcript": "ENST00000916104.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1118,
"aa_ref": "S",
"aa_start": 975,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5405,
"cdna_start": 3210,
"cds_end": null,
"cds_length": 3357,
"cds_start": 2924,
"consequences": [
"stop_gained"
],
"exon_count": 25,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000916107.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.2924C>A",
"hgvs_p": "p.Ser975*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586166.1",
"strand": true,
"transcript": "ENST00000916107.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1097,
"aa_ref": "S",
"aa_start": 954,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5494,
"cdna_start": 3049,
"cds_end": null,
"cds_length": 3294,
"cds_start": 2861,
"consequences": [
"stop_gained"
],
"exon_count": 25,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000916106.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.2861C>A",
"hgvs_p": "p.Ser954*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586165.1",
"strand": true,
"transcript": "ENST00000916106.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1129,
"aa_ref": "S",
"aa_start": 986,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5563,
"cdna_start": 3117,
"cds_end": null,
"cds_length": 3390,
"cds_start": 2957,
"consequences": [
"stop_gained"
],
"exon_count": 26,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_006714055.4",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.2957C>A",
"hgvs_p": "p.Ser986*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006714118.1",
"strand": true,
"transcript": "XM_006714055.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 783,
"aa_ref": "S",
"aa_start": 640,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4476,
"cdna_start": 2030,
"cds_end": null,
"cds_length": 2352,
"cds_start": 1919,
"consequences": [
"stop_gained"
],
"exon_count": 19,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_005265788.5",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.1919C>A",
"hgvs_p": "p.Ser640*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005265845.1",
"strand": true,
"transcript": "XM_005265788.5",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 630,
"aa_ref": "S",
"aa_start": 487,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4052,
"cdna_start": 1606,
"cds_end": null,
"cds_length": 1893,
"cds_start": 1460,
"consequences": [
"stop_gained"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011534412.2",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.1460C>A",
"hgvs_p": "p.Ser487*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532714.1",
"strand": true,
"transcript": "XM_011534412.2",
"transcript_support_level": null
},
{
"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": 3285,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000706801.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "n.1055C>A",
"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": "ENST00000706801.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs146076380",
"effect": "stop_gained",
"frequency_reference_population": 0.0000047937065,
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"gnomad_exomes_ac": 7,
"gnomad_exomes_af": 0.00000479371,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "not provided|Microcephaly 8, primary, autosomal recessive",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.558,
"pos": 56017835,
"ref": "C",
"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_025009.5"
}
]
}