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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: 5-148120311-G-GAAAA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=148120311&ref=G&alt=GAAAA&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "SPINK5",
"hgnc_id": 15464,
"hgvs_c": "c.2465_2468dupAAAA",
"hgvs_p": "p.Asp826fs",
"inheritance_mode": "AR",
"pathogenic_score": 10,
"score": 10,
"transcript": "NM_001127698.2",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "FBXO38-DT",
"hgnc_id": 55589,
"hgvs_c": "n.1257-26573_1257-26570dupTTTT",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000667608.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_score": 10,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "GAAAA",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 1064,
"aa_ref": "K",
"aa_start": 823,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3651,
"cdna_start": 2534,
"cds_end": null,
"cds_length": 3195,
"cds_start": 2469,
"consequences": [
"frameshift_variant"
],
"exon_count": 33,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "NM_006846.4",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.2465_2468dupAAAA",
"hgvs_p": "p.Asp826fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000256084.8",
"protein_coding": true,
"protein_id": "NP_006837.2",
"strand": true,
"transcript": "NM_006846.4",
"transcript_support_level": null
},
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 1064,
"aa_ref": "K",
"aa_start": 823,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3651,
"cdna_start": 2534,
"cds_end": null,
"cds_length": 3195,
"cds_start": 2469,
"consequences": [
"frameshift_variant"
],
"exon_count": 33,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000256084.8",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.2465_2468dupAAAA",
"hgvs_p": "p.Asp826fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006846.4",
"protein_coding": true,
"protein_id": "ENSP00000256084.7",
"strand": true,
"transcript": "ENST00000256084.8",
"transcript_support_level": 1
},
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 1094,
"aa_ref": "K",
"aa_start": 823,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3656,
"cdna_start": 2542,
"cds_end": null,
"cds_length": 3285,
"cds_start": 2469,
"consequences": [
"frameshift_variant"
],
"exon_count": 34,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000359874.7",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.2465_2468dupAAAA",
"hgvs_p": "p.Asp826fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000352936.3",
"strand": true,
"transcript": "ENST00000359874.7",
"transcript_support_level": 1
},
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 916,
"aa_ref": "K",
"aa_start": 823,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2915,
"cdna_start": 2542,
"cds_end": null,
"cds_length": 2751,
"cds_start": 2469,
"consequences": [
"frameshift_variant"
],
"exon_count": 28,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000398454.5",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.2465_2468dupAAAA",
"hgvs_p": "p.Asp826fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000381472.1",
"strand": true,
"transcript": "ENST00000398454.5",
"transcript_support_level": 1
},
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 1094,
"aa_ref": "K",
"aa_start": 823,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3741,
"cdna_start": 2534,
"cds_end": null,
"cds_length": 3285,
"cds_start": 2469,
"consequences": [
"frameshift_variant"
],
"exon_count": 34,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "NM_001127698.2",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.2465_2468dupAAAA",
"hgvs_p": "p.Asp826fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001121170.1",
"strand": true,
"transcript": "NM_001127698.2",
"transcript_support_level": null
},
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 916,
"aa_ref": "K",
"aa_start": 823,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2917,
"cdna_start": 2534,
"cds_end": null,
"cds_length": 2751,
"cds_start": 2469,
"consequences": [
"frameshift_variant"
],
"exon_count": 28,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "NM_001127699.2",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.2465_2468dupAAAA",
"hgvs_p": "p.Asp826fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001121171.1",
"strand": true,
"transcript": "NM_001127699.2",
"transcript_support_level": null
},
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 868,
"aa_ref": "K",
"aa_start": 804,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2674,
"cdna_start": 2477,
"cds_end": null,
"cds_length": 2609,
"cds_start": 2412,
"consequences": [
"frameshift_variant"
],
"exon_count": 27,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000508733.5",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.2408_2411dupAAAA",
"hgvs_p": "p.Asp807fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000421519.1",
"strand": true,
"transcript": "ENST00000508733.5",
"transcript_support_level": 5
},
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 1075,
"aa_ref": "K",
"aa_start": 804,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3684,
"cdna_start": 2477,
"cds_end": null,
"cds_length": 3228,
"cds_start": 2412,
"consequences": [
"frameshift_variant"
],
"exon_count": 34,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "XM_047416662.1",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.2408_2411dupAAAA",
"hgvs_p": "p.Asp807fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272618.1",
"strand": true,
"transcript": "XM_047416662.1",
"transcript_support_level": null
},
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 1066,
"aa_ref": "K",
"aa_start": 795,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3664,
"cdna_start": 2457,
"cds_end": null,
"cds_length": 3201,
"cds_start": 2385,
"consequences": [
"frameshift_variant"
],
"exon_count": 33,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "XM_011537551.3",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.2381_2384dupAAAA",
"hgvs_p": "p.Asp798fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011535853.1",
"strand": true,
"transcript": "XM_011537551.3",
"transcript_support_level": null
},
{
"aa_alt": "KK?",
"aa_end": null,
"aa_length": 842,
"aa_ref": "K",
"aa_start": 571,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3219,
"cdna_start": 2012,
"cds_end": null,
"cds_length": 2529,
"cds_start": 1713,
"consequences": [
"frameshift_variant"
],
"exon_count": 28,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_047416663.1",
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"hgvs_c": "c.1709_1712dupAAAA",
"hgvs_p": "p.Asp574fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272619.1",
"strand": true,
"transcript": "XM_047416663.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2991,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000667608.1",
"gene_hgnc_id": 55589,
"gene_symbol": "FBXO38-DT",
"hgvs_c": "n.1257-26573_1257-26570dupTTTT",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000667608.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs565782662",
"effect": "frameshift_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 15464,
"gene_symbol": "SPINK5",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 0,
"gnomad_genomes_af": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.935,
"pos": 148120311,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_001127698.2"
}
]
}