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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: 16-89935236-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=89935236&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 89935236,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000315491.12",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "c.785G>A",
"hgvs_p": "p.Arg262His",
"transcript": "NM_006086.4",
"protein_id": "NP_006077.2",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 450,
"cds_start": 785,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 845,
"cdna_end": null,
"cdna_length": 1706,
"mane_select": "ENST00000315491.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "c.785G>A",
"hgvs_p": "p.Arg262His",
"transcript": "ENST00000315491.12",
"protein_id": "ENSP00000320295.7",
"transcript_support_level": 1,
"aa_start": 262,
"aa_end": null,
"aa_length": 450,
"cds_start": 785,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 845,
"cdna_end": null,
"cdna_length": 1706,
"mane_select": "NM_006086.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000198211",
"gene_hgnc_id": null,
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Arg609His",
"transcript": "ENST00000556922.1",
"protein_id": "ENSP00000451560.1",
"transcript_support_level": 2,
"aa_start": 609,
"aa_end": null,
"aa_length": 797,
"cds_start": 1826,
"cds_end": null,
"cds_length": 2394,
"cdna_start": 1920,
"cdna_end": null,
"cdna_length": 2776,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "c.569G>A",
"hgvs_p": "p.Arg190His",
"transcript": "NM_001197181.2",
"protein_id": "NP_001184110.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 378,
"cds_start": 569,
"cds_end": null,
"cds_length": 1137,
"cdna_start": 1049,
"cdna_end": null,
"cdna_length": 1910,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "c.569G>A",
"hgvs_p": "p.Arg190His",
"transcript": "ENST00000554444.5",
"protein_id": "ENSP00000451617.1",
"transcript_support_level": 2,
"aa_start": 190,
"aa_end": null,
"aa_length": 378,
"cds_start": 569,
"cds_end": null,
"cds_length": 1137,
"cdna_start": 1123,
"cdna_end": null,
"cdna_length": 1978,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "n.*870G>A",
"hgvs_p": null,
"transcript": "ENST00000555609.5",
"protein_id": "ENSP00000451276.1",
"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": 1855,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "n.4206G>A",
"hgvs_p": null,
"transcript": "ENST00000680788.1",
"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": 5062,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "n.*870G>A",
"hgvs_p": null,
"transcript": "ENST00000555609.5",
"protein_id": "ENSP00000451276.1",
"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": 1855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "c.277+1658G>A",
"hgvs_p": null,
"transcript": "ENST00000555576.5",
"protein_id": "ENSP00000452554.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 97,
"cds_start": -4,
"cds_end": null,
"cds_length": 294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "c.*1G>A",
"hgvs_p": null,
"transcript": "ENST00000555810.5",
"protein_id": "ENSP00000450538.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 188,
"cds_start": -4,
"cds_end": null,
"cds_length": 568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 767,
"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": "TUBB3",
"gene_hgnc_id": 20772,
"hgvs_c": "n.*584G>A",
"hgvs_p": null,
"transcript": "ENST00000556536.5",
"protein_id": "ENSP00000451378.1",
"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": 925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TUBB3",
"gene_hgnc_id": 20772,
"dbsnp": "rs864321716",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9941666126251221,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.872,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9962,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.824,
"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": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000315491.12",
"gene_symbol": "TUBB3",
"hgnc_id": 20772,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.785G>A",
"hgvs_p": "p.Arg262His"
},
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000556922.1",
"gene_symbol": "ENSG00000198211",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Arg609His"
}
],
"clinvar_disease": " 3A, congenital, with or without extraocular involvement,Fibrosis of extraocular muscles,TUBB3-related disorder,TUBB3-related tubulinopathy,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7 LP:2 O:1",
"phenotype_combined": "Fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement|not provided|TUBB3-related tubulinopathy|TUBB3-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}