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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: 16-1791032-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=1791032&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "IGFALS",
"hgnc_id": 5468,
"hgvs_c": "c.1500C>T",
"hgvs_p": "p.Tyr500Tyr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_001146006.2",
"verdict": "Benign"
},
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "SPSB3",
"hgnc_id": 30629,
"hgvs_c": "c.-13+2605C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "ENST00000569769.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_score": -21,
"allele_count_reference_population": 205476,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"chr": "16",
"clinvar_classification": "Benign",
"clinvar_disease": "Short stature due to primary acid-labile subunit deficiency,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6700000166893005,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 605,
"aa_ref": "Y",
"aa_start": 462,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2058,
"cdna_start": 1439,
"cds_end": null,
"cds_length": 1818,
"cds_start": 1386,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_004970.3",
"gene_hgnc_id": 5468,
"gene_symbol": "IGFALS",
"hgvs_c": "c.1386C>T",
"hgvs_p": "p.Tyr462Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000215539.4",
"protein_coding": true,
"protein_id": "NP_004961.1",
"strand": false,
"transcript": "NM_004970.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 605,
"aa_ref": "Y",
"aa_start": 462,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2058,
"cdna_start": 1439,
"cds_end": null,
"cds_length": 1818,
"cds_start": 1386,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000215539.4",
"gene_hgnc_id": 5468,
"gene_symbol": "IGFALS",
"hgvs_c": "c.1386C>T",
"hgvs_p": "p.Tyr462Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004970.3",
"protein_coding": true,
"protein_id": "ENSP00000215539.3",
"strand": false,
"transcript": "ENST00000215539.4",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 643,
"aa_ref": "Y",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2172,
"cdna_start": 1553,
"cds_end": null,
"cds_length": 1932,
"cds_start": 1500,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001146006.2",
"gene_hgnc_id": 5468,
"gene_symbol": "IGFALS",
"hgvs_c": "c.1500C>T",
"hgvs_p": "p.Tyr500Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001139478.1",
"strand": false,
"transcript": "NM_001146006.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 643,
"aa_ref": "Y",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2136,
"cdna_start": 1580,
"cds_end": null,
"cds_length": 1932,
"cds_start": 1500,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000415638.3",
"gene_hgnc_id": 5468,
"gene_symbol": "IGFALS",
"hgvs_c": "c.1500C>T",
"hgvs_p": "p.Tyr500Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000416683.3",
"strand": false,
"transcript": "ENST00000415638.3",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 630,
"aa_ref": "Y",
"aa_start": 487,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2155,
"cdna_start": 1539,
"cds_end": null,
"cds_length": 1893,
"cds_start": 1461,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000897144.1",
"gene_hgnc_id": 5468,
"gene_symbol": "IGFALS",
"hgvs_c": "c.1461C>T",
"hgvs_p": "p.Tyr487Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000567203.1",
"strand": false,
"transcript": "ENST00000897144.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 604,
"aa_ref": "Y",
"aa_start": 461,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2077,
"cdna_start": 1465,
"cds_end": null,
"cds_length": 1815,
"cds_start": 1383,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000897145.1",
"gene_hgnc_id": 5468,
"gene_symbol": "IGFALS",
"hgvs_c": "c.1383C>T",
"hgvs_p": "p.Tyr461Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000567204.1",
"strand": false,
"transcript": "ENST00000897145.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 167,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 580,
"cdna_start": null,
"cds_end": null,
"cds_length": 504,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000569769.1",
"gene_hgnc_id": 30629,
"gene_symbol": "SPSB3",
"hgvs_c": "c.-13+2605C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000455098.1",
"strand": false,
"transcript": "ENST00000569769.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2059,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NR_027389.1",
"gene_hgnc_id": 5468,
"gene_symbol": "IGFALS",
"hgvs_c": "n.1440C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_027389.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs17559",
"effect": "synonymous_variant",
"frequency_reference_population": 0.12856457,
"gene_hgnc_id": 5468,
"gene_symbol": "IGFALS",
"gnomad_exomes_ac": 175051,
"gnomad_exomes_af": 0.121057,
"gnomad_exomes_homalt": 14844,
"gnomad_genomes_ac": 30425,
"gnomad_genomes_af": 0.199883,
"gnomad_genomes_homalt": 4936,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 19780,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "Short stature due to primary acid-labile subunit deficiency|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.71,
"pos": 1791032,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001146006.2"
}
]
}