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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: 17-16003885-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=16003885&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 16003885,
"ref": "C",
"alt": "T",
"effect": "stop_gained,splice_region_variant",
"transcript": "ENST00000261647.10",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Gln173*",
"transcript": "NM_017775.4",
"protein_id": "NP_060245.3",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 380,
"cds_start": 517,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 3050,
"mane_select": "ENST00000261647.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Gln173*",
"transcript": "ENST00000261647.10",
"protein_id": "ENSP00000261647.5",
"transcript_support_level": 1,
"aa_start": 173,
"aa_end": null,
"aa_length": 380,
"cds_start": 517,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 3050,
"mane_select": "NM_017775.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "c.196C>T",
"hgvs_p": "p.Gln66*",
"transcript": "NM_001271420.2",
"protein_id": "NP_001258349.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 273,
"cds_start": 196,
"cds_end": null,
"cds_length": 822,
"cdna_start": 679,
"cdna_end": null,
"cdna_length": 3187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Gln173*",
"transcript": "XM_017024801.3",
"protein_id": "XP_016880290.2",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 348,
"cds_start": 517,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 1532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Gln173*",
"transcript": "XM_017024802.3",
"protein_id": "XP_016880291.2",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 335,
"cds_start": 517,
"cds_end": null,
"cds_length": 1008,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 1590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Gln173*",
"transcript": "XM_024450814.2",
"protein_id": "XP_024306582.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 234,
"cds_start": 517,
"cds_end": null,
"cds_length": 705,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "n.*337C>T",
"hgvs_p": null,
"transcript": "ENST00000466729.5",
"protein_id": "ENSP00000466261.1",
"transcript_support_level": 5,
"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": 908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "n.*201C>T",
"hgvs_p": null,
"transcript": "ENST00000475723.5",
"protein_id": "ENSP00000465754.1",
"transcript_support_level": 2,
"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": 2591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "n.627C>T",
"hgvs_p": null,
"transcript": "ENST00000497842.6",
"protein_id": null,
"transcript_support_level": 5,
"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": 1360,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "n.*337C>T",
"hgvs_p": null,
"transcript": "ENST00000466729.5",
"protein_id": "ENSP00000466261.1",
"transcript_support_level": 5,
"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": 908,
"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": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "n.*201C>T",
"hgvs_p": null,
"transcript": "ENST00000475723.5",
"protein_id": "ENSP00000465754.1",
"transcript_support_level": 2,
"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": 2591,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"hgvs_c": "n.*218C>T",
"hgvs_p": null,
"transcript": "ENST00000470399.1",
"protein_id": "ENSP00000465082.1",
"transcript_support_level": 5,
"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": 636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TTC19",
"gene_hgnc_id": 26006,
"dbsnp": "rs387907094",
"frequency_reference_population": 6.842519e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84252e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5199999809265137,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.7559999823570251,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.215,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.31,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.998382374581505,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP3",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000261647.10",
"gene_symbol": "TTC19",
"hgnc_id": 26006,
"effects": [
"stop_gained",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Gln173*"
}
],
"clinvar_disease": "Mitochondrial complex III deficiency nuclear type 2",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Mitochondrial complex III deficiency nuclear type 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}