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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: 5-135033794-CG-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=135033794&ref=CG&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 135033794,
"ref": "CG",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "NM_002653.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX1",
"gene_hgnc_id": 9004,
"hgvs_c": "c.87delC",
"hgvs_p": "p.Ala30fs",
"transcript": "NM_002653.5",
"protein_id": "NP_002644.4",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 314,
"cds_start": 87,
"cds_end": null,
"cds_length": 945,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 2337,
"mane_select": "ENST00000265340.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX1",
"gene_hgnc_id": 9004,
"hgvs_c": "c.87delC",
"hgvs_p": "p.Ala30fs",
"transcript": "ENST00000265340.12",
"protein_id": "ENSP00000265340.6",
"transcript_support_level": 1,
"aa_start": 29,
"aa_end": null,
"aa_length": 314,
"cds_start": 87,
"cds_end": null,
"cds_length": 945,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 2337,
"mane_select": "NM_002653.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX1",
"gene_hgnc_id": 9004,
"hgvs_c": "c.87delC",
"hgvs_p": "p.Ala30fs",
"transcript": "ENST00000506438.5",
"protein_id": "ENSP00000427542.1",
"transcript_support_level": 1,
"aa_start": 29,
"aa_end": null,
"aa_length": 314,
"cds_start": 87,
"cds_end": null,
"cds_length": 945,
"cdna_start": 221,
"cdna_end": null,
"cdna_length": 1305,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX1",
"gene_hgnc_id": 9004,
"hgvs_c": "c.87delC",
"hgvs_p": "p.Ala30fs",
"transcript": "ENST00000507253.5",
"protein_id": "ENSP00000422908.1",
"transcript_support_level": 3,
"aa_start": 29,
"aa_end": null,
"aa_length": 129,
"cds_start": 87,
"cds_end": null,
"cds_length": 392,
"cdna_start": 282,
"cdna_end": null,
"cdna_length": 587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX1",
"gene_hgnc_id": 9004,
"hgvs_c": "c.87delC",
"hgvs_p": "p.Ala30fs",
"transcript": "ENST00000502676.1",
"protein_id": "ENSP00000423624.1",
"transcript_support_level": 3,
"aa_start": 29,
"aa_end": null,
"aa_length": 113,
"cds_start": 87,
"cds_end": null,
"cds_length": 342,
"cdna_start": 411,
"cdna_end": null,
"cdna_length": 666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX1",
"gene_hgnc_id": 9004,
"hgvs_c": "c.189delC",
"hgvs_p": "p.Ala64fs",
"transcript": "XM_047417318.1",
"protein_id": "XP_047273274.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 348,
"cds_start": 189,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 443,
"cdna_end": null,
"cdna_length": 2346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PITX1-AS1",
"gene_hgnc_id": 48332,
"hgvs_c": "n.99+257delG",
"hgvs_p": null,
"transcript": "ENST00000505828.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PITX1-AS1",
"gene_hgnc_id": 48332,
"hgvs_c": "n.159+257delG",
"hgvs_p": null,
"transcript": "ENST00000507641.5",
"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": 547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PITX1-AS1",
"gene_hgnc_id": 48332,
"hgvs_c": "n.261+257delG",
"hgvs_p": null,
"transcript": "ENST00000624272.3",
"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": 2479,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PITX1-AS1",
"gene_hgnc_id": 48332,
"hgvs_c": "n.119+257delG",
"hgvs_p": null,
"transcript": "ENST00000806983.1",
"protein_id": null,
"transcript_support_level": null,
"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": 877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PITX1-AS1",
"gene_hgnc_id": 48332,
"hgvs_c": "n.267+257delG",
"hgvs_p": null,
"transcript": "NR_161235.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PITX1",
"gene_hgnc_id": 9004,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.508,
"phylop100way_prediction": "Benign",
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_002653.5",
"gene_symbol": "PITX1",
"hgnc_id": 9004,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.87delC",
"hgvs_p": "p.Ala30fs"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000624272.3",
"gene_symbol": "PITX1-AS1",
"hgnc_id": 48332,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.261+257delG",
"hgvs_p": null
}
],
"clinvar_disease": "Clubfoot",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Clubfoot",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}