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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: 9-128633791-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=128633791&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 128633791,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_052844.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.1564C>T",
"hgvs_p": "p.Arg522Trp",
"transcript": "NM_052844.4",
"protein_id": "NP_443076.2",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 536,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1685,
"cdna_end": null,
"cdna_length": 1823,
"mane_select": "ENST00000372715.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.1564C>T",
"hgvs_p": "p.Arg522Trp",
"transcript": "ENST00000372715.7",
"protein_id": "ENSP00000361800.2",
"transcript_support_level": 1,
"aa_start": 522,
"aa_end": null,
"aa_length": 536,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1685,
"cdna_end": null,
"cdna_length": 1823,
"mane_select": "NM_052844.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.1564C>T",
"hgvs_p": "p.Arg522Trp",
"transcript": "XM_047424057.1",
"protein_id": "XP_047280013.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 536,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1791,
"cdna_end": null,
"cdna_length": 1929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.1480C>T",
"hgvs_p": "p.Arg494Trp",
"transcript": "XM_011519179.3",
"protein_id": "XP_011517481.1",
"transcript_support_level": null,
"aa_start": 494,
"aa_end": null,
"aa_length": 508,
"cds_start": 1480,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 1707,
"cdna_end": null,
"cdna_length": 1845,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTAN1",
"gene_hgnc_id": 11273,
"hgvs_c": "c.*457G>A",
"hgvs_p": null,
"transcript": "NM_001130438.3",
"protein_id": "NP_001123910.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2477,
"cds_start": -4,
"cds_end": null,
"cds_length": 7434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7875,
"mane_select": "ENST00000372739.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTAN1",
"gene_hgnc_id": 11273,
"hgvs_c": "c.*457G>A",
"hgvs_p": null,
"transcript": "ENST00000372739.7",
"protein_id": "ENSP00000361824.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2477,
"cds_start": -4,
"cds_end": null,
"cds_length": 7434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7875,
"mane_select": "NM_001130438.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTAN1",
"gene_hgnc_id": 11273,
"hgvs_c": "c.*457G>A",
"hgvs_p": null,
"transcript": "ENST00000372731.8",
"protein_id": "ENSP00000361816.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2472,
"cds_start": -4,
"cds_end": null,
"cds_length": 7419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTAN1",
"gene_hgnc_id": 11273,
"hgvs_c": "c.*457G>A",
"hgvs_p": null,
"transcript": "ENST00000358161.9",
"protein_id": "ENSP00000350882.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2452,
"cds_start": -4,
"cds_end": null,
"cds_length": 7359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTAN1",
"gene_hgnc_id": 11273,
"hgvs_c": "c.*457G>A",
"hgvs_p": null,
"transcript": "NM_001375318.1",
"protein_id": "NP_001362247.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2510,
"cds_start": -4,
"cds_end": null,
"cds_length": 7533,
"cdna_start": null,
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"cdna_length": 8604,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
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"exon_count": 58,
"intron_rank": null,
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"gene_symbol": "SPTAN1",
"gene_hgnc_id": 11273,
"hgvs_c": "c.*457G>A",
"hgvs_p": null,
"transcript": "NM_001375310.1",
"protein_id": "NP_001362239.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2506,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
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"gene_symbol": "SPTAN1",
"gene_hgnc_id": 11273,
"hgvs_c": "c.*457G>A",
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"transcript": "ENST00000704202.1",
"protein_id": "ENSP00000515764.1",
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"cds_start": -4,
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"cdna_start": null,
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},
{
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"consequences": [
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],
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"gene_symbol": "SPTAN1",
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"hgvs_c": "c.*457G>A",
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},
{
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"strand": true,
"consequences": [
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],
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"intron_rank": null,
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"gene_symbol": "SPTAN1",
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"hgvs_c": "c.*457G>A",
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"transcript": "NM_001438445.1",
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},
{
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"strand": true,
"consequences": [
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],
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"gene_symbol": "SPTAN1",
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},
{
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],
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"gene_symbol": "SPTAN1",
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"hgvs_c": "c.*457G>A",
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"transcript": "NM_001438440.1",
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},
{
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],
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"gene_symbol": "SPTAN1",
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"hgvs_c": "c.*457G>A",
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},
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],
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"gene_symbol": "SPTAN1",
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},
{
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],
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"gene_symbol": "SPTAN1",
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},
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],
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],
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": null,
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"gene_symbol": "SPTAN1",
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"hgvs_c": "c.*457G>A",
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"transcript": "NM_001375313.1",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 55,
"intron_rank": null,
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"gene_symbol": "SPTAN1",
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"hgvs_c": "c.*457G>A",
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"cdna_end": null,
"cdna_length": 7833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"dbsnp": "rs368864898",
"frequency_reference_population": 0.000027269269,
"hom_count_reference_population": 1,
"allele_count_reference_population": 44,
"gnomad_exomes_af": 0.0000260056,
"gnomad_genomes_af": 0.0000393928,
"gnomad_exomes_ac": 38,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5971976518630981,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.411,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1248,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.565,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_052844.4",
"gene_symbol": "DYNC2I2",
"hgnc_id": 28296,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1564C>T",
"hgvs_p": "p.Arg522Trp"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001130438.3",
"gene_symbol": "SPTAN1",
"hgnc_id": 11273,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.*457G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Short-rib thoracic dysplasia 11 with or without polydactyly",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Short-rib thoracic dysplasia 11 with or without polydactyly",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}