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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: 2-219250479-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=219250479&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 219250479,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_006000.3",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBA4A",
"gene_hgnc_id": 12407,
"hgvs_c": "c.1220G>A",
"hgvs_p": "p.Trp407*",
"transcript": "NM_006000.3",
"protein_id": "NP_005991.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 448,
"cds_start": 1220,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000248437.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006000.3"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBA4A",
"gene_hgnc_id": 12407,
"hgvs_c": "c.1220G>A",
"hgvs_p": "p.Trp407*",
"transcript": "ENST00000248437.9",
"protein_id": "ENSP00000248437.4",
"transcript_support_level": 1,
"aa_start": 407,
"aa_end": null,
"aa_length": 448,
"cds_start": 1220,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006000.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000248437.9"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBA4A",
"gene_hgnc_id": 12407,
"hgvs_c": "c.1226G>A",
"hgvs_p": "p.Trp409*",
"transcript": "ENST00000875456.1",
"protein_id": "ENSP00000545515.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 450,
"cds_start": 1226,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875456.1"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBA4A",
"gene_hgnc_id": 12407,
"hgvs_c": "c.1175G>A",
"hgvs_p": "p.Trp392*",
"transcript": "NM_001278552.2",
"protein_id": "NP_001265481.1",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 433,
"cds_start": 1175,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278552.2"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBA4A",
"gene_hgnc_id": 12407,
"hgvs_c": "c.1175G>A",
"hgvs_p": "p.Trp392*",
"transcript": "ENST00000392088.6",
"protein_id": "ENSP00000375938.2",
"transcript_support_level": 2,
"aa_start": 392,
"aa_end": null,
"aa_length": 433,
"cds_start": 1175,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392088.6"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBA4A",
"gene_hgnc_id": 12407,
"hgvs_c": "c.1247G>A",
"hgvs_p": "p.Trp416*",
"transcript": "XM_047445674.1",
"protein_id": "XP_047301630.1",
"transcript_support_level": null,
"aa_start": 416,
"aa_end": null,
"aa_length": 457,
"cds_start": 1247,
"cds_end": null,
"cds_length": 1374,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445674.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "NM_001330213.2",
"protein_id": "NP_001317142.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 305,
"cds_start": null,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000396738.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330213.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "ENST00000396738.7",
"protein_id": "ENSP00000379964.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 305,
"cds_start": null,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001330213.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396738.7"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "ENST00000409638.7",
"protein_id": "ENSP00000386928.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 305,
"cds_start": null,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409638.7"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "ENST00000875263.1",
"protein_id": "ENSP00000545322.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": null,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875263.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "NM_001008910.4",
"protein_id": "NP_001008910.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 305,
"cds_start": null,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001008910.4"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "ENST00000875262.1",
"protein_id": "ENSP00000545321.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 305,
"cds_start": null,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875262.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "NM_001330214.1",
"protein_id": "NP_001317143.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330214.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "NM_001330215.2",
"protein_id": "NP_001317144.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 187,
"cds_start": null,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330215.2"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "XM_024453195.2",
"protein_id": "XP_024308963.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453195.2"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "XM_047446140.1",
"protein_id": "XP_047302096.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446140.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK16",
"gene_hgnc_id": 11394,
"hgvs_c": "c.*1920C>T",
"hgvs_p": null,
"transcript": "XM_047446141.1",
"protein_id": "XP_047302097.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": null,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446141.1"
},
{
"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": "TUBA4A",
"gene_hgnc_id": 12407,
"hgvs_c": "n.*250G>A",
"hgvs_p": null,
"transcript": "ENST00000498660.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000498660.1"
}
],
"gene_symbol": "TUBA4A",
"gene_hgnc_id": 12407,
"dbsnp": "rs730880027",
"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": 0.5799999833106995,
"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": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.879,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006000.3",
"gene_symbol": "TUBA4A",
"hgnc_id": 12407,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.1220G>A",
"hgvs_p": "p.Trp407*"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001008910.4",
"gene_symbol": "STK16",
"hgnc_id": 11394,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.*1920C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Amyotrophic lateral sclerosis type 22",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Amyotrophic lateral sclerosis type 22",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}