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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: 17-39672828-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=39672828&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 39672828,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_033419.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "NM_033419.5",
"protein_id": "NP_219487.3",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 320,
"cds_start": 938,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000300658.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_033419.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "ENST00000300658.9",
"protein_id": "ENSP00000300658.4",
"transcript_support_level": 1,
"aa_start": 313,
"aa_end": null,
"aa_length": 320,
"cds_start": 938,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_033419.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000300658.9"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.875C>T",
"hgvs_p": "p.Ser292Leu",
"transcript": "NM_001291728.2",
"protein_id": "NP_001278657.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 299,
"cds_start": 875,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291728.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.875C>T",
"hgvs_p": "p.Ser292Leu",
"transcript": "ENST00000429199.6",
"protein_id": "ENSP00000415765.2",
"transcript_support_level": 2,
"aa_start": 292,
"aa_end": null,
"aa_length": 299,
"cds_start": 875,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000429199.6"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.785C>T",
"hgvs_p": "p.Ser262Leu",
"transcript": "NM_001291726.2",
"protein_id": "NP_001278655.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 269,
"cds_start": 785,
"cds_end": null,
"cds_length": 810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291726.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.785C>T",
"hgvs_p": "p.Ser262Leu",
"transcript": "ENST00000378011.8",
"protein_id": "ENSP00000367250.4",
"transcript_support_level": 2,
"aa_start": 262,
"aa_end": null,
"aa_length": 269,
"cds_start": 785,
"cds_end": null,
"cds_length": 810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378011.8"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.596C>T",
"hgvs_p": "p.Ser199Leu",
"transcript": "NM_001291730.2",
"protein_id": "NP_001278659.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 206,
"cds_start": 596,
"cds_end": null,
"cds_length": 621,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291730.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"transcript": "NM_001291732.2",
"protein_id": "NP_001278661.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 185,
"cds_start": 533,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291732.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Ser198Leu",
"transcript": "XM_047437082.1",
"protein_id": "XP_047293038.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 205,
"cds_start": 593,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437082.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.-137C>T",
"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": null,
"cds_end": null,
"cds_length": 723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000619169.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.*24C>T",
"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": null,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291733.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.*24C>T",
"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": null,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000579146.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.*7C>T",
"hgvs_p": null,
"transcript": "XM_011525480.2",
"protein_id": "XP_011523782.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 241,
"cds_start": null,
"cds_end": null,
"cds_length": 726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011525480.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "n.1323C>T",
"hgvs_p": null,
"transcript": "ENST00000309862.10",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000309862.10"
}
],
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"dbsnp": "rs1036625226",
"frequency_reference_population": 0.000030358302,
"hom_count_reference_population": 0,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000300993,
"gnomad_genomes_af": 0.0000328459,
"gnomad_exomes_ac": 44,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06473678350448608,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.095,
"revel_prediction": "Benign",
"alphamissense_score": 0.1168,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.704,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_033419.5",
"gene_symbol": "PGAP3",
"hgnc_id": 23719,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}