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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: 12-101786012-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=101786012&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 101786012,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000299314.12",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Val191Ile",
"transcript": "NM_024312.5",
"protein_id": "NP_077288.2",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 1256,
"cds_start": 571,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 855,
"cdna_end": null,
"cdna_length": 5720,
"mane_select": "ENST00000299314.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Val191Ile",
"transcript": "ENST00000299314.12",
"protein_id": "ENSP00000299314.7",
"transcript_support_level": 1,
"aa_start": 191,
"aa_end": null,
"aa_length": 1256,
"cds_start": 571,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 855,
"cdna_end": null,
"cdna_length": 5720,
"mane_select": "NM_024312.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Val191Ile",
"transcript": "ENST00000549940.5",
"protein_id": "ENSP00000449150.1",
"transcript_support_level": 1,
"aa_start": 191,
"aa_end": null,
"aa_length": 490,
"cds_start": 571,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 714,
"cdna_end": null,
"cdna_length": 1678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.205G>A",
"hgvs_p": "p.Val69Ile",
"transcript": "ENST00000552681.1",
"protein_id": "ENSP00000449217.1",
"transcript_support_level": 1,
"aa_start": 69,
"aa_end": null,
"aa_length": 138,
"cds_start": 205,
"cds_end": null,
"cds_length": 417,
"cdna_start": 205,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.490G>A",
"hgvs_p": "p.Val164Ile",
"transcript": "XM_011538731.3",
"protein_id": "XP_011537033.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 1229,
"cds_start": 490,
"cds_end": null,
"cds_length": 3690,
"cdna_start": 506,
"cdna_end": null,
"cdna_length": 5371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Val191Ile",
"transcript": "XM_006719593.4",
"protein_id": "XP_006719656.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 1179,
"cds_start": 571,
"cds_end": null,
"cds_length": 3540,
"cdna_start": 855,
"cdna_end": null,
"cdna_length": 4070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "n.365G>A",
"hgvs_p": null,
"transcript": "ENST00000550352.1",
"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": 787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"dbsnp": "rs751953529",
"frequency_reference_population": 6.897218e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.89722e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3242190480232239,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9900000095367432,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.436,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1004,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.609,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.84,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999989401404497,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000299314.12",
"gene_symbol": "GNPTAB",
"hgnc_id": 29670,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Val191Ile"
}
],
"clinvar_disease": "Mucolipidosis type II,Pseudo-Hurler polydystrophy",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Mucolipidosis type II;Pseudo-Hurler polydystrophy",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}