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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: 2-43805247-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=43805247&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 43805247,
"ref": "G",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "ENST00000260605.12",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.943G>A",
"hgvs_p": "p.Val315Ile",
"transcript": "ENST00000378587.3",
"protein_id": "ENSP00000367850.3",
"transcript_support_level": 1,
"aa_start": 315,
"aa_end": null,
"aa_length": 317,
"cds_start": 943,
"cds_end": null,
"cds_length": 954,
"cdna_start": 945,
"cdna_end": null,
"cdna_length": 1253,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.993+1G>A",
"hgvs_p": null,
"transcript": "NM_016008.4",
"protein_id": "NP_057092.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 351,
"cds_start": -4,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1399,
"mane_select": "ENST00000260605.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.993+1G>A",
"hgvs_p": null,
"transcript": "ENST00000260605.12",
"protein_id": "ENSP00000260605.8",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 351,
"cds_start": -4,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1399,
"mane_select": "NM_016008.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.996+1G>A",
"hgvs_p": null,
"transcript": "ENST00000605786.5",
"protein_id": "ENSP00000474032.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 352,
"cds_start": -4,
"cds_end": null,
"cds_length": 1059,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1346,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.996+1G>A",
"hgvs_p": null,
"transcript": "NM_001348913.2",
"protein_id": "NP_001335842.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 374,
"cds_start": -4,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2202,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.993+1G>A",
"hgvs_p": null,
"transcript": "NM_001348912.2",
"protein_id": "NP_001335841.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 373,
"cds_start": -4,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2199,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "c.996+1G>A",
"hgvs_p": null,
"transcript": "NM_001193464.2",
"protein_id": "NP_001180393.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 352,
"cds_start": -4,
"cds_end": null,
"cds_length": 1059,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1402,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"hgvs_c": "n.*70G>A",
"hgvs_p": null,
"transcript": "ENST00000482738.1",
"protein_id": null,
"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": 561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DYNC2LI1",
"gene_hgnc_id": 24595,
"dbsnp": "rs374356079",
"frequency_reference_population": 0.000022052913,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000236941,
"gnomad_genomes_af": 0.00000657307,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3199999928474426,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.871999979019165,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.797,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.92,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999981674494154,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Moderate,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000260605.12",
"gene_symbol": "DYNC2LI1",
"hgnc_id": 24595,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.993+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Asphyxiating thoracic dystrophy 1,Short-rib thoracic dysplasia 15 with polydactyly,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Short-rib thoracic dysplasia 15 with polydactyly|Asphyxiating thoracic dystrophy 1|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}