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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: 5-13717389-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=13717389&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 13717389,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000265104.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 73,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12631G>T",
"hgvs_p": "p.Glu4211*",
"transcript": "NM_001369.3",
"protein_id": "NP_001360.1",
"transcript_support_level": null,
"aa_start": 4211,
"aa_end": null,
"aa_length": 4624,
"cds_start": 12631,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 12881,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "ENST00000265104.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 73,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12631G>T",
"hgvs_p": "p.Glu4211*",
"transcript": "ENST00000265104.5",
"protein_id": "ENSP00000265104.4",
"transcript_support_level": 1,
"aa_start": 4211,
"aa_end": null,
"aa_length": 4624,
"cds_start": 12631,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 12881,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "NM_001369.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 73,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12586G>T",
"hgvs_p": "p.Glu4196*",
"transcript": "ENST00000681290.1",
"protein_id": "ENSP00000505288.1",
"transcript_support_level": null,
"aa_start": 4196,
"aa_end": null,
"aa_length": 4609,
"cds_start": 12586,
"cds_end": null,
"cds_length": 13830,
"cdna_start": 12745,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 73,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12739G>T",
"hgvs_p": "p.Glu4247*",
"transcript": "XM_005248262.4",
"protein_id": "XP_005248319.2",
"transcript_support_level": null,
"aa_start": 4247,
"aa_end": null,
"aa_length": 4660,
"cds_start": 12739,
"cds_end": null,
"cds_length": 13983,
"cdna_start": 12745,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 73,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12391G>T",
"hgvs_p": "p.Glu4131*",
"transcript": "XM_047416886.1",
"protein_id": "XP_047272842.1",
"transcript_support_level": null,
"aa_start": 4131,
"aa_end": null,
"aa_length": 4544,
"cds_start": 12391,
"cds_end": null,
"cds_length": 13635,
"cdna_start": 13510,
"cdna_end": null,
"cdna_length": 16410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 73,
"exon_rank_end": null,
"exon_count": 77,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12739G>T",
"hgvs_p": "p.Glu4247*",
"transcript": "XM_017009177.2",
"protein_id": "XP_016864666.1",
"transcript_support_level": null,
"aa_start": 4247,
"aa_end": null,
"aa_length": 4520,
"cds_start": 12739,
"cds_end": null,
"cds_length": 13563,
"cdna_start": 12745,
"cdna_end": null,
"cdna_length": 15225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 67,
"exon_rank_end": null,
"exon_count": 73,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.11644G>T",
"hgvs_p": "p.Glu3882*",
"transcript": "XM_017009179.3",
"protein_id": "XP_016864668.1",
"transcript_support_level": null,
"aa_start": 3882,
"aa_end": null,
"aa_length": 4295,
"cds_start": 11644,
"cds_end": null,
"cds_length": 12888,
"cdna_start": 11853,
"cdna_end": null,
"cdna_length": 14753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 73,
"exon_rank_end": null,
"exon_count": 74,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12739G>T",
"hgvs_p": "p.Glu4247*",
"transcript": "XM_017009180.2",
"protein_id": "XP_016864669.1",
"transcript_support_level": null,
"aa_start": 4247,
"aa_end": null,
"aa_length": 4272,
"cds_start": 12739,
"cds_end": null,
"cds_length": 12819,
"cdna_start": 12745,
"cdna_end": null,
"cdna_length": 12932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.7828G>T",
"hgvs_p": "p.Glu2610*",
"transcript": "XM_017009185.1",
"protein_id": "XP_016864674.1",
"transcript_support_level": null,
"aa_start": 2610,
"aa_end": null,
"aa_length": 3023,
"cds_start": 7828,
"cds_end": null,
"cds_length": 9072,
"cdna_start": 8052,
"cdna_end": null,
"cdna_length": 10952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.7381G>T",
"hgvs_p": "p.Glu2461*",
"transcript": "XM_017009186.2",
"protein_id": "XP_016864675.1",
"transcript_support_level": null,
"aa_start": 2461,
"aa_end": null,
"aa_length": 2874,
"cds_start": 7381,
"cds_end": null,
"cds_length": 8625,
"cdna_start": 7483,
"cdna_end": null,
"cdna_length": 10383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.6718G>T",
"hgvs_p": "p.Glu2240*",
"transcript": "XM_017009188.2",
"protein_id": "XP_016864677.1",
"transcript_support_level": null,
"aa_start": 2240,
"aa_end": null,
"aa_length": 2653,
"cds_start": 6718,
"cds_end": null,
"cds_length": 7962,
"cdna_start": 8285,
"cdna_end": null,
"cdna_length": 11185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"dbsnp": "rs762673561",
"frequency_reference_population": 0.000014251228,
"hom_count_reference_population": 0,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.00001505,
"gnomad_genomes_af": 0.00000657454,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6499999761581421,
"computational_prediction_selected": "Pathogenic",
"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": "Pathogenic",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000265104.5",
"gene_symbol": "DNAH5",
"hgnc_id": 2950,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.12631G>T",
"hgvs_p": "p.Glu4211*"
}
],
"clinvar_disease": "Primary ciliary dyskinesia,Primary ciliary dyskinesia 3",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Primary ciliary dyskinesia|Primary ciliary dyskinesia 3",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}