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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: 1-160283029-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=160283029&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 14,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "PEX19",
"hgnc_id": 9713,
"hgvs_c": "c.261C>T",
"hgvs_p": "p.Phe87Phe",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -14,
"transcript": "NM_002857.4",
"verdict": "Benign"
},
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000258465",
"hgnc_id": null,
"hgvs_c": "n.*28C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -9,
"transcript": "ENST00000556710.6",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS1,BS2",
"acmg_score": -14,
"allele_count_reference_population": 5039,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.65,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "PEX19-related disorder,Peroxisome biogenesis disorder 12A (Zellweger),not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6499999761581421,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 299,
"aa_ref": "F",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3653,
"cdna_start": 270,
"cds_end": null,
"cds_length": 900,
"cds_start": 261,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_002857.4",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "c.261C>T",
"hgvs_p": "p.Phe87Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000368072.10",
"protein_coding": true,
"protein_id": "NP_002848.1",
"strand": false,
"transcript": "NM_002857.4",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 299,
"aa_ref": "F",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3653,
"cdna_start": 270,
"cds_end": null,
"cds_length": 900,
"cds_start": 261,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000368072.10",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "c.261C>T",
"hgvs_p": "p.Phe87Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002857.4",
"protein_coding": true,
"protein_id": "ENSP00000357051.5",
"strand": false,
"transcript": "ENST00000368072.10",
"transcript_support_level": 1
},
{
"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": 3504,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000472750.5",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.*28C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000434633.1",
"strand": false,
"transcript": "ENST00000472750.5",
"transcript_support_level": 1
},
{
"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": 3504,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000472750.5",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.*28C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000434633.1",
"strand": false,
"transcript": "ENST00000472750.5",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 337,
"aa_ref": "F",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3699,
"cdna_start": 269,
"cds_end": null,
"cds_length": 1014,
"cds_start": 261,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000920352.1",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "c.261C>T",
"hgvs_p": "p.Phe87Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590411.1",
"strand": false,
"transcript": "ENST00000920352.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 307,
"aa_ref": "F",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2004,
"cdna_start": 273,
"cds_end": null,
"cds_length": 924,
"cds_start": 261,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000920353.1",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "c.261C>T",
"hgvs_p": "p.Phe87Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590412.1",
"strand": false,
"transcript": "ENST00000920353.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 279,
"aa_ref": "F",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3617,
"cdna_start": 288,
"cds_end": null,
"cds_length": 840,
"cds_start": 261,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001193644.1",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "c.261C>T",
"hgvs_p": "p.Phe87Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001180573.1",
"strand": false,
"transcript": "NM_001193644.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 269,
"aa_ref": "F",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1888,
"cdna_start": 272,
"cds_end": null,
"cds_length": 810,
"cds_start": 261,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000857246.1",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "c.261C>T",
"hgvs_p": "p.Phe87Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000527305.1",
"strand": false,
"transcript": "ENST00000857246.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 234,
"aa_ref": "F",
"aa_start": 67,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 796,
"cdna_start": 292,
"cds_end": null,
"cds_length": 705,
"cds_start": 201,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000392220.2",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "c.201C>T",
"hgvs_p": "p.Phe67Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000376054.2",
"strand": false,
"transcript": "ENST00000392220.2",
"transcript_support_level": 5
},
{
"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": 904,
"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": "ENST00000462644.5",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.201C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000435896.1",
"strand": false,
"transcript": "ENST00000462644.5",
"transcript_support_level": 3
},
{
"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": 548,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000524939.1",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.278C>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": "ENST00000524939.1",
"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": 1237,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000532508.5",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.233C>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": "ENST00000532508.5",
"transcript_support_level": 5
},
{
"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": 894,
"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": "ENST00000532643.5",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.261C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000435915.1",
"strand": false,
"transcript": "ENST00000532643.5",
"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": 544,
"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": "ENST00000533104.1",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.160C>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": "ENST00000533104.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"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": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000533699.5",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.255C>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": "ENST00000533699.5",
"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": 2635,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000556710.6",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258465",
"hgvs_c": "n.*28C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000451235.2",
"strand": false,
"transcript": "ENST00000556710.6",
"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": 3543,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NR_036492.2",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.160C>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": "NR_036492.2",
"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": 3567,
"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": "NR_036493.2",
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"hgvs_c": "n.270C>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": "NR_036493.2",
"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": 2635,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000556710.6",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258465",
"hgvs_c": "n.*28C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000451235.2",
"strand": false,
"transcript": "ENST00000556710.6",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs146644725",
"effect": "synonymous_variant",
"frequency_reference_population": 0.003121821,
"gene_hgnc_id": 9713,
"gene_symbol": "PEX19",
"gnomad_exomes_ac": 4728,
"gnomad_exomes_af": 0.00323423,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_ac": 311,
"gnomad_genomes_af": 0.00204256,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 8,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Peroxisome biogenesis disorder 12A (Zellweger)|PEX19-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.441,
"pos": 160283029,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002857.4"
}
]
}