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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: 17-41809745-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=41809745&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 41809745,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000393928.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H4",
"gene_hgnc_id": 16946,
"hgvs_c": "c.877G>A",
"hgvs_p": "p.Ala293Thr",
"transcript": "NM_006455.3",
"protein_id": "NP_006446.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 437,
"cds_start": 877,
"cds_end": null,
"cds_length": 1314,
"cdna_start": 911,
"cdna_end": null,
"cdna_length": 2352,
"mane_select": "ENST00000393928.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H4",
"gene_hgnc_id": 16946,
"hgvs_c": "c.877G>A",
"hgvs_p": "p.Ala293Thr",
"transcript": "ENST00000393928.6",
"protein_id": "ENSP00000377505.1",
"transcript_support_level": 1,
"aa_start": 293,
"aa_end": null,
"aa_length": 437,
"cds_start": 877,
"cds_end": null,
"cds_length": 1314,
"cdna_start": 911,
"cdna_end": null,
"cdna_length": 2352,
"mane_select": "NM_006455.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H4",
"gene_hgnc_id": 16946,
"hgvs_c": "c.877G>A",
"hgvs_p": "p.Ala293Thr",
"transcript": "ENST00000355468.7",
"protein_id": "ENSP00000347649.2",
"transcript_support_level": 2,
"aa_start": 293,
"aa_end": null,
"aa_length": 437,
"cds_start": 877,
"cds_end": null,
"cds_length": 1314,
"cdna_start": 1344,
"cdna_end": null,
"cdna_length": 2791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H4",
"gene_hgnc_id": 16946,
"hgvs_c": "c.1060G>A",
"hgvs_p": "p.Ala354Thr",
"transcript": "XM_047435137.1",
"protein_id": "XP_047291093.1",
"transcript_support_level": null,
"aa_start": 354,
"aa_end": null,
"aa_length": 498,
"cds_start": 1060,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 1094,
"cdna_end": null,
"cdna_length": 2535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H4",
"gene_hgnc_id": 16946,
"hgvs_c": "c.1060G>A",
"hgvs_p": "p.Ala354Thr",
"transcript": "XM_047435138.1",
"protein_id": "XP_047291094.1",
"transcript_support_level": null,
"aa_start": 354,
"aa_end": null,
"aa_length": 494,
"cds_start": 1060,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 1094,
"cdna_end": null,
"cdna_length": 2390,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H4",
"gene_hgnc_id": 16946,
"hgvs_c": "c.877G>A",
"hgvs_p": "p.Ala293Thr",
"transcript": "XM_006721640.5",
"protein_id": "XP_006721703.2",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 433,
"cds_start": 877,
"cds_end": null,
"cds_length": 1302,
"cdna_start": 911,
"cdna_end": null,
"cdna_length": 2207,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "P3H4",
"gene_hgnc_id": 16946,
"hgvs_c": "c.430+1118G>A",
"hgvs_p": null,
"transcript": "ENST00000592026.1",
"protein_id": "ENSP00000468174.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 219,
"cds_start": -4,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "P3H4",
"gene_hgnc_id": 16946,
"hgvs_c": "n.481+935G>A",
"hgvs_p": null,
"transcript": "ENST00000587455.1",
"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": 536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "P3H4",
"gene_hgnc_id": 16946,
"dbsnp": "rs782698241",
"frequency_reference_population": 0.000027268627,
"hom_count_reference_population": 0,
"allele_count_reference_population": 44,
"gnomad_exomes_af": 0.0000287393,
"gnomad_genomes_af": 0.0000131441,
"gnomad_exomes_ac": 42,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7908228039741516,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.297,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8741,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.979,
"phylop100way_prediction": "Uncertain_significance",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000393928.6",
"gene_symbol": "P3H4",
"hgnc_id": 16946,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.877G>A",
"hgvs_p": "p.Ala293Thr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}