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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: 4-88065803-AGTAC-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=88065803&ref=AGTAC&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "PKD2",
"hgnc_id": 9009,
"hgvs_c": "c.2284_2287delTACG",
"hgvs_p": "p.Tyr762fs",
"inheritance_mode": "AD,AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_000297.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_score": 12,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "4",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Multicystic kidney dysplasia,Polycystic kidney disease,Polycystic kidney disease 2,Polycystic liver disease 1",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:2",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 968,
"aa_ref": "YD",
"aa_start": 762,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5089,
"cdna_start": 2383,
"cds_end": null,
"cds_length": 2907,
"cds_start": 2284,
"consequences": [
"frameshift_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_000297.4",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.2284_2287delTACG",
"hgvs_p": "p.Tyr762fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000237596.7",
"protein_coding": true,
"protein_id": "NP_000288.1",
"strand": true,
"transcript": "NM_000297.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 968,
"aa_ref": "YD",
"aa_start": 762,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5089,
"cdna_start": 2383,
"cds_end": null,
"cds_length": 2907,
"cds_start": 2284,
"consequences": [
"frameshift_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000237596.7",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.2284_2287delTACG",
"hgvs_p": "p.Tyr762fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000297.4",
"protein_coding": true,
"protein_id": "ENSP00000237596.2",
"strand": true,
"transcript": "ENST00000237596.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 967,
"aa_ref": "YD",
"aa_start": 762,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5089,
"cdna_start": 2389,
"cds_end": null,
"cds_length": 2904,
"cds_start": 2284,
"consequences": [
"frameshift_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000927447.1",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.2284_2287delTACG",
"hgvs_p": "p.Tyr762fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000597506.1",
"strand": true,
"transcript": "ENST00000927447.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 935,
"aa_ref": "YD",
"aa_start": 729,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4990,
"cdna_start": 2287,
"cds_end": null,
"cds_length": 2808,
"cds_start": 2185,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000927448.1",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.2185_2188delTACG",
"hgvs_p": "p.Tyr729fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000597507.1",
"strand": true,
"transcript": "ENST00000927448.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 929,
"aa_ref": "YD",
"aa_start": 724,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4956,
"cdna_start": 2257,
"cds_end": null,
"cds_length": 2790,
"cds_start": 2170,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000956200.1",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.2170_2173delTACG",
"hgvs_p": "p.Tyr724fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626259.1",
"strand": true,
"transcript": "ENST00000956200.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 893,
"aa_ref": "YD",
"aa_start": 687,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4864,
"cdna_start": 2158,
"cds_end": null,
"cds_length": 2682,
"cds_start": 2059,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001440544.1",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.2059_2062delTACG",
"hgvs_p": "p.Tyr687fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001427473.1",
"strand": true,
"transcript": "NM_001440544.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 775,
"aa_ref": "YD",
"aa_start": 569,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4510,
"cdna_start": 1804,
"cds_end": null,
"cds_length": 2328,
"cds_start": 1705,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000956199.1",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.1705_1708delTACG",
"hgvs_p": "p.Tyr569fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626258.1",
"strand": true,
"transcript": "ENST00000956199.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 386,
"aa_ref": "YD",
"aa_start": 180,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1222,
"cdna_start": 588,
"cds_end": null,
"cds_length": 1161,
"cds_start": 538,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000502363.1",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.538_541delTACG",
"hgvs_p": "p.Tyr180fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000425289.1",
"strand": true,
"transcript": "ENST00000502363.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 386,
"aa_ref": "YD",
"aa_start": 180,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1720,
"cdna_start": 933,
"cds_end": null,
"cds_length": 1161,
"cds_start": 538,
"consequences": [
"frameshift_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000508588.5",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.538_541delTACG",
"hgvs_p": "p.Tyr180fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000427131.1",
"strand": true,
"transcript": "ENST00000508588.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 728,
"aa_ref": "YD",
"aa_start": 522,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4367,
"cdna_start": 1661,
"cds_end": null,
"cds_length": 2187,
"cds_start": 1564,
"consequences": [
"frameshift_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011532029.2",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.1564_1567delTACG",
"hgvs_p": "p.Tyr522fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530331.1",
"strand": true,
"transcript": "XM_011532029.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 688,
"aa_ref": "YD",
"aa_start": 482,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4409,
"cdna_start": 1703,
"cds_end": null,
"cds_length": 2067,
"cds_start": 1444,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011532030.3",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "c.1444_1447delTACG",
"hgvs_p": "p.Tyr482fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530332.1",
"strand": true,
"transcript": "XM_011532030.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1362,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000511337.5",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "n.536_539delTACG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000511337.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1554,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000512858.1",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "n.762_765delTACG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000512858.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4968,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NR_156488.2",
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"hgvs_c": "n.2262_2265delTACG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_156488.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1553927823",
"effect": "frameshift_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 9009,
"gene_symbol": "PKD2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Multicystic kidney dysplasia;Polycystic kidney disease;Polycystic liver disease 1|Polycystic kidney disease 2",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.768,
"pos": 88065803,
"ref": "AGTAC",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_000297.4"
}
]
}