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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: 17-39684715-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=39684715&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PGAP3",
"hgnc_id": 23719,
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"inheritance_mode": "AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_033419.5",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate",
"acmg_score": 6,
"allele_count_reference_population": 10,
"alphamissense_prediction": null,
"alphamissense_score": 0.7491,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.42,
"chr": "17",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8573435544967651,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 320,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2687,
"cdna_start": 357,
"cds_end": null,
"cds_length": 963,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_033419.5",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000300658.9",
"protein_coding": true,
"protein_id": "NP_219487.3",
"strand": false,
"transcript": "NM_033419.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 320,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2687,
"cdna_start": 357,
"cds_end": null,
"cds_length": 963,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000300658.9",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_033419.5",
"protein_coding": true,
"protein_id": "ENSP00000300658.4",
"strand": false,
"transcript": "ENST00000300658.9",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 299,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2624,
"cdna_start": 357,
"cds_end": null,
"cds_length": 900,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001291728.2",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278657.1",
"strand": false,
"transcript": "NM_001291728.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 299,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 970,
"cdna_start": 357,
"cds_end": null,
"cds_length": 900,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000429199.6",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000415765.2",
"strand": false,
"transcript": "ENST00000429199.6",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 206,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2345,
"cdna_start": 357,
"cds_end": null,
"cds_length": 621,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001291730.2",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278659.1",
"strand": false,
"transcript": "NM_001291730.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 185,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2282,
"cdna_start": 357,
"cds_end": null,
"cds_length": 558,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001291732.2",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278661.1",
"strand": false,
"transcript": "NM_001291732.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 148,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2220,
"cdna_start": 357,
"cds_end": null,
"cds_length": 447,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001291733.2",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278662.1",
"strand": false,
"transcript": "NM_001291733.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 148,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2220,
"cdna_start": 357,
"cds_end": null,
"cds_length": 447,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000579146.5",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000463234.1",
"strand": false,
"transcript": "ENST00000579146.5",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 69,
"aa_ref": "P",
"aa_start": 33,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 538,
"cdna_start": 425,
"cds_end": null,
"cds_length": 211,
"cds_start": 98,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000584856.1",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.98C>T",
"hgvs_p": "p.Pro33Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000463785.1",
"strand": false,
"transcript": "ENST00000584856.1",
"transcript_support_level": 4
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 241,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2482,
"cdna_start": 357,
"cds_end": null,
"cds_length": 726,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011525480.2",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523782.1",
"strand": false,
"transcript": "XM_011525480.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 154,
"aa_ref": "P",
"aa_start": 105,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 596,
"cdna_start": 357,
"cds_end": null,
"cds_length": 465,
"cds_start": 314,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047437083.1",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.314C>T",
"hgvs_p": "p.Pro105Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047293039.1",
"strand": false,
"transcript": "XM_047437083.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 269,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2534,
"cdna_start": null,
"cds_end": null,
"cds_length": 810,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001291726.2",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.279+1207C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278655.1",
"strand": false,
"transcript": "NM_001291726.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 269,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2533,
"cdna_start": null,
"cds_end": null,
"cds_length": 810,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000378011.8",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.279+1207C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000367250.4",
"strand": false,
"transcript": "ENST00000378011.8",
"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": 3028,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000309862.10",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "n.357C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000309862.10",
"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": 556,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000580898.5",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "n.191C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000580898.5",
"transcript_support_level": 4
},
{
"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": 546,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000582276.1",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "n.251C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000582276.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 804,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000584620.5",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "n.299C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000463011.1",
"strand": false,
"transcript": "ENST00000584620.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 240,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2094,
"cdna_start": null,
"cds_end": null,
"cds_length": 723,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000619169.4",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.-624C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000478028.1",
"strand": true,
"transcript": "ENST00000619169.4",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 205,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2444,
"cdna_start": null,
"cds_end": null,
"cds_length": 618,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047437082.1",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "c.-174C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047293038.1",
"strand": true,
"transcript": "XM_047437082.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 587,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000577337.5",
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"hgvs_c": "n.-17C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000464308.1",
"strand": true,
"transcript": "ENST00000577337.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs371549948",
"effect": "missense_variant",
"frequency_reference_population": 0.000006203797,
"gene_hgnc_id": 23719,
"gene_symbol": "PGAP3",
"gnomad_exomes_ac": 8,
"gnomad_exomes_af": 0.00000548071,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131363,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.659,
"pos": 39684715,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.49,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_033419.5"
}
]
}