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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: X-38421026-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=38421026&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 38421026,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000531.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Val337Leu",
"transcript": "NM_000531.6",
"protein_id": "NP_000522.3",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 354,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 1102,
"cdna_end": null,
"cdna_length": 1522,
"mane_select": "ENST00000039007.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Val337Leu",
"transcript": "ENST00000039007.5",
"protein_id": "ENSP00000039007.4",
"transcript_support_level": 1,
"aa_start": 337,
"aa_end": null,
"aa_length": 354,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 1102,
"cdna_end": null,
"cdna_length": 1522,
"mane_select": "NM_000531.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250349",
"gene_hgnc_id": null,
"hgvs_c": "c.172-245095G>C",
"hgvs_p": null,
"transcript": "ENST00000465127.1",
"protein_id": "ENSP00000417050.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 279,
"cds_start": -4,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Val337Leu",
"transcript": "NM_001407092.1",
"protein_id": "NP_001394021.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 354,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 1379,
"cdna_end": null,
"cdna_length": 3281,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Val337Leu",
"transcript": "ENST00000713758.1",
"protein_id": "ENSP00000519059.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 354,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 1465,
"cdna_end": null,
"cdna_length": 3347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "c.844G>C",
"hgvs_p": "p.Val282Leu",
"transcript": "ENST00000713759.1",
"protein_id": "ENSP00000519060.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 299,
"cds_start": 844,
"cds_end": null,
"cds_length": 900,
"cdna_start": 1126,
"cdna_end": null,
"cdna_length": 2672,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "n.*759G>C",
"hgvs_p": null,
"transcript": "ENST00000643344.1",
"protein_id": "ENSP00000496606.1",
"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": 1304,
"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": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "n.*771G>C",
"hgvs_p": null,
"transcript": "ENST00000713760.1",
"protein_id": "ENSP00000519061.1",
"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": 3373,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "n.*759G>C",
"hgvs_p": null,
"transcript": "ENST00000643344.1",
"protein_id": "ENSP00000496606.1",
"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": 1304,
"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": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"hgvs_c": "n.*771G>C",
"hgvs_p": null,
"transcript": "ENST00000713760.1",
"protein_id": "ENSP00000519061.1",
"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": 3373,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OTC",
"gene_hgnc_id": 8512,
"dbsnp": "rs72558487",
"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": 0.933905303478241,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.618,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3623,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.032,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000531.6",
"gene_symbol": "OTC",
"hgnc_id": 8512,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Val337Leu"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000465127.1",
"gene_symbol": "ENSG00000250349",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.172-245095G>C",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}