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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: 17-39674647-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=39674647&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 39674647,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000300658.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.465T>C",
"hgvs_p": "p.Val155Val",
"transcript": "NM_033419.5",
"protein_id": "NP_219487.3",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 320,
"cds_start": 465,
"cds_end": null,
"cds_length": 963,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 2687,
"mane_select": "ENST00000300658.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.465T>C",
"hgvs_p": "p.Val155Val",
"transcript": "ENST00000300658.9",
"protein_id": "ENSP00000300658.4",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 320,
"cds_start": 465,
"cds_end": null,
"cds_length": 963,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 2687,
"mane_select": "NM_033419.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.312T>C",
"hgvs_p": "p.Val104Val",
"transcript": "NM_001291726.2",
"protein_id": "NP_001278655.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 269,
"cds_start": 312,
"cds_end": null,
"cds_length": 810,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.312T>C",
"hgvs_p": "p.Val104Val",
"transcript": "ENST00000378011.8",
"protein_id": "ENSP00000367250.4",
"transcript_support_level": 2,
"aa_start": 104,
"aa_end": null,
"aa_length": 269,
"cds_start": 312,
"cds_end": null,
"cds_length": 810,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 2533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.465T>C",
"hgvs_p": "p.Val155Val",
"transcript": "NM_001291730.2",
"protein_id": "NP_001278659.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 206,
"cds_start": 465,
"cds_end": null,
"cds_length": 621,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 2345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.465T>C",
"hgvs_p": "p.Val155Val",
"transcript": "XM_011525480.2",
"protein_id": "XP_011523782.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 241,
"cds_start": 465,
"cds_end": null,
"cds_length": 726,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 2482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.120T>C",
"hgvs_p": "p.Val40Val",
"transcript": "XM_047437082.1",
"protein_id": "XP_047293038.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 205,
"cds_start": 120,
"cds_end": null,
"cds_length": 618,
"cdna_start": 265,
"cdna_end": null,
"cdna_length": 2444,
"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": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "n.508T>C",
"hgvs_p": null,
"transcript": "ENST00000309862.10",
"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": 3028,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "n.*142T>C",
"hgvs_p": null,
"transcript": "ENST00000577337.5",
"protein_id": "ENSP00000464308.1",
"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": 587,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "n.342T>C",
"hgvs_p": null,
"transcript": "ENST00000580898.5",
"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": 556,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "n.402T>C",
"hgvs_p": null,
"transcript": "ENST00000582276.1",
"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": 546,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "n.*142T>C",
"hgvs_p": null,
"transcript": "ENST00000584620.5",
"protein_id": "ENSP00000463011.1",
"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": 804,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.-473T>C",
"hgvs_p": null,
"transcript": "ENST00000619169.4",
"protein_id": "ENSP00000478028.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 240,
"cds_start": -4,
"cds_end": null,
"cds_length": 723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "n.*142T>C",
"hgvs_p": null,
"transcript": "ENST00000577337.5",
"protein_id": "ENSP00000464308.1",
"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": 587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "n.*142T>C",
"hgvs_p": null,
"transcript": "ENST00000584620.5",
"protein_id": "ENSP00000463011.1",
"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": 804,
"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": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.433-593T>C",
"hgvs_p": null,
"transcript": "NM_001291728.2",
"protein_id": "NP_001278657.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2624,
"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": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.433-593T>C",
"hgvs_p": null,
"transcript": "ENST00000429199.6",
"protein_id": "ENSP00000415765.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 970,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.433-593T>C",
"hgvs_p": null,
"transcript": "NM_001291732.2",
"protein_id": "NP_001278661.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 185,
"cds_start": -4,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2282,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.433-1781T>C",
"hgvs_p": null,
"transcript": "NM_001291733.2",
"protein_id": "NP_001278662.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 148,
"cds_start": -4,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2220,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.433-1781T>C",
"hgvs_p": null,
"transcript": "ENST00000579146.5",
"protein_id": "ENSP00000463234.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 148,
"cds_start": -4,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"dbsnp": "rs2941504",
"frequency_reference_population": 0.6858756,
"hom_count_reference_population": 367720,
"allele_count_reference_population": 1062933,
"gnomad_exomes_af": 0.69116,
"gnomad_genomes_af": 0.637279,
"gnomad_exomes_ac": 966073,
"gnomad_genomes_ac": 96860,
"gnomad_exomes_homalt": 336307,
"gnomad_genomes_homalt": 31413,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6600000262260437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.069,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000300658.9",
"gene_symbol": "PGAP3",
"hgnc_id": 23719,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.465T>C",
"hgvs_p": "p.Val155Val"
}
],
"clinvar_disease": "Hyperphosphatasia with intellectual disability syndrome 4,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not provided|Hyperphosphatasia with intellectual disability syndrome 4",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}