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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: 2-131478358-G-GTT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=131478358&ref=G&alt=GTT&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 131478358,
"ref": "G",
"alt": "GTT",
"effect": "frameshift_variant",
"transcript": "ENST00000321253.7",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBA3D",
"gene_hgnc_id": 24071,
"hgvs_c": "c.200_201dupTT",
"hgvs_p": "p.Val68fs",
"transcript": "NM_080386.4",
"protein_id": "NP_525125.2",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 450,
"cds_start": 202,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 283,
"cdna_end": null,
"cdna_length": 1520,
"mane_select": "ENST00000321253.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TUBA3D",
"gene_hgnc_id": 24071,
"hgvs_c": "c.200_201dupTT",
"hgvs_p": "p.Val68fs",
"transcript": "ENST00000321253.7",
"protein_id": "ENSP00000326042.6",
"transcript_support_level": 1,
"aa_start": 68,
"aa_end": null,
"aa_length": 450,
"cds_start": 202,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 283,
"cdna_end": null,
"cdna_length": 1520,
"mane_select": "NM_080386.4",
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MZT2A",
"gene_hgnc_id": 33187,
"hgvs_c": "n.278-6178_278-6177dupAA",
"hgvs_p": null,
"transcript": "ENST00000427024.5",
"protein_id": "ENSP00000403353.1",
"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": 679,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MZT2A",
"gene_hgnc_id": 33187,
"hgvs_c": "n.331-6178_331-6177dupAA",
"hgvs_p": null,
"transcript": "ENST00000445782.2",
"protein_id": null,
"transcript_support_level": 2,
"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": 980,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MZT2A",
"gene_hgnc_id": 33187,
"hgvs_c": "c.623-6178_623-6177dupAA",
"hgvs_p": null,
"transcript": "XM_047445568.1",
"protein_id": "XP_047301524.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 254,
"cds_start": -4,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1494,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MZT2A",
"gene_hgnc_id": 33187,
"hgvs_c": "c.320-6178_320-6177dupAA",
"hgvs_p": null,
"transcript": "XM_005263742.4",
"protein_id": "XP_005263799.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": -4,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1071,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TUBA3D",
"gene_hgnc_id": 24071,
"dbsnp": "rs756938019",
"frequency_reference_population": 0.000013129563,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000752648,
"gnomad_genomes_af": 0.0000131296,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 5.367,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000321253.7",
"gene_symbol": "TUBA3D",
"hgnc_id": 24071,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.200_201dupTT",
"hgvs_p": "p.Val68fs"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000445782.2",
"gene_symbol": "MZT2A",
"hgnc_id": 33187,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.331-6178_331-6177dupAA",
"hgvs_p": null
}
],
"clinvar_disease": "Keratoconus 9",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Keratoconus 9",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}