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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: 4-1003397-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=1003397&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 1003397,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000514224.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.1577T>C",
"hgvs_p": "p.Leu526Pro",
"transcript": "NM_000203.5",
"protein_id": "NP_000194.2",
"transcript_support_level": null,
"aa_start": 526,
"aa_end": null,
"aa_length": 653,
"cds_start": 1577,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 1618,
"cdna_end": null,
"cdna_length": 2174,
"mane_select": "ENST00000514224.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.1577T>C",
"hgvs_p": "p.Leu526Pro",
"transcript": "ENST00000514224.2",
"protein_id": "ENSP00000425081.2",
"transcript_support_level": 2,
"aa_start": 526,
"aa_end": null,
"aa_length": 653,
"cds_start": 1577,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 1618,
"cdna_end": null,
"cdna_length": 2174,
"mane_select": "NM_000203.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.1577T>C",
"hgvs_p": "p.Leu526Pro",
"transcript": "ENST00000247933.9",
"protein_id": "ENSP00000247933.4",
"transcript_support_level": 1,
"aa_start": 526,
"aa_end": null,
"aa_length": 653,
"cds_start": 1577,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 1665,
"cdna_end": null,
"cdna_length": 2186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.1181T>C",
"hgvs_p": "p.Leu394Pro",
"transcript": "NM_001363576.1",
"protein_id": "NP_001350505.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 521,
"cds_start": 1181,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 1633,
"cdna_end": null,
"cdna_length": 2182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.1764T>C",
"hgvs_p": "p.Pro588Pro",
"transcript": "XM_047415650.1",
"protein_id": "XP_047271606.1",
"transcript_support_level": null,
"aa_start": 588,
"aa_end": null,
"aa_length": 632,
"cds_start": 1764,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1852,
"cdna_end": null,
"cdna_length": 2099,
"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": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.1684T>C",
"hgvs_p": null,
"transcript": "ENST00000514698.5",
"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": 2185,
"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": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.1633T>C",
"hgvs_p": null,
"transcript": "ENST00000652070.1",
"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": 2130,
"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": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.1665T>C",
"hgvs_p": null,
"transcript": "NR_110313.1",
"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": 2218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.-32T>C",
"hgvs_p": null,
"transcript": "ENST00000514417.1",
"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": 218,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.*8T>C",
"hgvs_p": null,
"transcript": "ENST00000502829.1",
"protein_id": null,
"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": 558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"dbsnp": "rs781136336",
"frequency_reference_population": 0.00039083385,
"hom_count_reference_population": 0,
"allele_count_reference_population": 595,
"gnomad_exomes_af": 0.000404243,
"gnomad_genomes_af": 0.000269875,
"gnomad_exomes_ac": 554,
"gnomad_genomes_ac": 41,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8571418523788452,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.774,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.387,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.43,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.819,
"phylop100way_prediction": "Benign",
"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": "PM3,PP4,PP3_Moderate",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM3",
"PP4",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000514224.2",
"gene_symbol": "IDUA",
"hgnc_id": 5391,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1577T>C",
"hgvs_p": "p.Leu526Pro"
}
],
"clinvar_disease": " MPS-I-H/S, MPS-I-S,Hurler syndrome,Mucopolysaccharidosis,Mucopolysaccharidosis type 1,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:1 LP:3 US:3",
"phenotype_combined": "Mucopolysaccharidosis type 1|not provided|Mucopolysaccharidosis, MPS-I-H/S|Mucopolysaccharidosis, MPS-I-S;Hurler syndrome;Mucopolysaccharidosis, MPS-I-H/S",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}