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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: 4-183684059-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=183684059&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 183684059,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000334690.11",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"hgvs_c": "c.1287+5G>A",
"hgvs_p": null,
"transcript": "NM_021942.6",
"protein_id": "NP_068761.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1133,
"cds_start": -4,
"cds_end": null,
"cds_length": 3402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4523,
"mane_select": "ENST00000334690.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"hgvs_c": "c.1287+5G>A",
"hgvs_p": null,
"transcript": "ENST00000334690.11",
"protein_id": "ENSP00000335371.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1133,
"cds_start": -4,
"cds_end": null,
"cds_length": 3402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4523,
"mane_select": "NM_021942.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"hgvs_c": "c.1287+5G>A",
"hgvs_p": null,
"transcript": "ENST00000357207.8",
"protein_id": "ENSP00000349738.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1086,
"cds_start": -4,
"cds_end": null,
"cds_length": 3261,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4435,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"hgvs_c": "c.105+5G>A",
"hgvs_p": null,
"transcript": "ENST00000512476.1",
"protein_id": "ENSP00000421004.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 739,
"cds_start": -4,
"cds_end": null,
"cds_length": 2220,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"hgvs_c": "n.348+53G>A",
"hgvs_p": null,
"transcript": "ENST00000505676.5",
"protein_id": "ENSP00000422915.1",
"transcript_support_level": 1,
"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": 2244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"hgvs_c": "c.1287+5G>A",
"hgvs_p": null,
"transcript": "NM_199053.3",
"protein_id": "NP_951008.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1086,
"cds_start": -4,
"cds_end": null,
"cds_length": 3261,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"hgvs_c": "c.1287+5G>A",
"hgvs_p": null,
"transcript": "XM_024454179.2",
"protein_id": "XP_024309947.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1133,
"cds_start": -4,
"cds_end": null,
"cds_length": 3402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"hgvs_c": "c.1287+5G>A",
"hgvs_p": null,
"transcript": "XM_024454180.2",
"protein_id": "XP_024309948.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1133,
"cds_start": -4,
"cds_end": null,
"cds_length": 3402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"hgvs_c": "c.1287+5G>A",
"hgvs_p": null,
"transcript": "XM_047416069.1",
"protein_id": "XP_047272025.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1019,
"cds_start": -4,
"cds_end": null,
"cds_length": 3060,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3311,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRAPPC11",
"gene_hgnc_id": 25751,
"dbsnp": "rs397509418",
"frequency_reference_population": 0.000038432358,
"hom_count_reference_population": 0,
"allele_count_reference_population": 62,
"gnomad_exomes_af": 0.0000383278,
"gnomad_genomes_af": 0.0000394368,
"gnomad_exomes_ac": 56,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.20999999344348907,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9980000257492065,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.699,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.65,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999981023438699,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000334690.11",
"gene_symbol": "TRAPPC11",
"hgnc_id": 25751,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1287+5G>A",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive 23, limb-girdle,Autosomal recessive limb-girdle muscular dystrophy type R18,Muscular dystrophy,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:9 LP:1",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type R18|not provided|Muscular dystrophy, limb-girdle, autosomal recessive 23",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}