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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: 7-92501648-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=92501648&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 92501648,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000248633.9",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.2442C>T",
"hgvs_p": "p.Phe814Phe",
"transcript": "NM_000466.3",
"protein_id": "NP_000457.1",
"transcript_support_level": null,
"aa_start": 814,
"aa_end": null,
"aa_length": 1283,
"cds_start": 2442,
"cds_end": null,
"cds_length": 3852,
"cdna_start": 2527,
"cdna_end": null,
"cdna_length": 4369,
"mane_select": "ENST00000248633.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.2442C>T",
"hgvs_p": "p.Phe814Phe",
"transcript": "ENST00000248633.9",
"protein_id": "ENSP00000248633.4",
"transcript_support_level": 1,
"aa_start": 814,
"aa_end": null,
"aa_length": 1283,
"cds_start": 2442,
"cds_end": null,
"cds_length": 3852,
"cdna_start": 2527,
"cdna_end": null,
"cdna_length": 4369,
"mane_select": "NM_000466.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.2271C>T",
"hgvs_p": "p.Phe757Phe",
"transcript": "ENST00000428214.5",
"protein_id": "ENSP00000394413.1",
"transcript_support_level": 1,
"aa_start": 757,
"aa_end": null,
"aa_length": 1226,
"cds_start": 2271,
"cds_end": null,
"cds_length": 3681,
"cdna_start": 2271,
"cdna_end": null,
"cdna_length": 3681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.2271C>T",
"hgvs_p": "p.Phe757Phe",
"transcript": "NM_001282677.2",
"protein_id": "NP_001269606.1",
"transcript_support_level": null,
"aa_start": 757,
"aa_end": null,
"aa_length": 1226,
"cds_start": 2271,
"cds_end": null,
"cds_length": 3681,
"cdna_start": 2356,
"cdna_end": null,
"cdna_length": 4198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.1818C>T",
"hgvs_p": "p.Phe606Phe",
"transcript": "NM_001282678.2",
"protein_id": "NP_001269607.1",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 1075,
"cds_start": 1818,
"cds_end": null,
"cds_length": 3228,
"cdna_start": 2562,
"cdna_end": null,
"cdna_length": 4404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.1476C>T",
"hgvs_p": "p.Phe492Phe",
"transcript": "ENST00000438045.5",
"protein_id": "ENSP00000410438.1",
"transcript_support_level": 2,
"aa_start": 492,
"aa_end": null,
"aa_length": 961,
"cds_start": 1476,
"cds_end": null,
"cds_length": 2886,
"cdna_start": 1482,
"cdna_end": null,
"cdna_length": 3329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.2442C>T",
"hgvs_p": "p.Phe814Phe",
"transcript": "XM_047420472.1",
"protein_id": "XP_047276428.1",
"transcript_support_level": null,
"aa_start": 814,
"aa_end": null,
"aa_length": 1227,
"cds_start": 2442,
"cds_end": null,
"cds_length": 3684,
"cdna_start": 2527,
"cdna_end": null,
"cdna_length": 3846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.693C>T",
"hgvs_p": "p.Phe231Phe",
"transcript": "XM_047420473.1",
"protein_id": "XP_047276429.1",
"transcript_support_level": null,
"aa_start": 231,
"aa_end": null,
"aa_length": 700,
"cds_start": 693,
"cds_end": null,
"cds_length": 2103,
"cdna_start": 861,
"cdna_end": null,
"cdna_length": 2703,
"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": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "n.2481C>T",
"hgvs_p": null,
"transcript": "ENST00000484913.5",
"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": 4051,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "n.2334C>T",
"hgvs_p": null,
"transcript": "ENST00000496420.5",
"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": 5333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000244055",
"gene_hgnc_id": null,
"hgvs_c": "n.154-17994G>A",
"hgvs_p": null,
"transcript": "ENST00000746412.1",
"protein_id": null,
"transcript_support_level": null,
"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": 389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "n.*120C>T",
"hgvs_p": null,
"transcript": "ENST00000496092.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"dbsnp": "rs145430946",
"frequency_reference_population": 0.0028294486,
"hom_count_reference_population": 16,
"allele_count_reference_population": 4566,
"gnomad_exomes_af": 0.00288672,
"gnomad_genomes_af": 0.00227954,
"gnomad_exomes_ac": 4219,
"gnomad_genomes_ac": 347,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4000000059604645,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.622,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000248633.9",
"gene_symbol": "PEX1",
"hgnc_id": 8850,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2442C>T",
"hgvs_p": "p.Phe814Phe"
},
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000746412.1",
"gene_symbol": "ENSG00000244055",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.154-17994G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Peroxisome biogenesis disorder 1A (Zellweger),Zellweger spectrum disorders,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:2",
"phenotype_combined": "not specified|Peroxisome biogenesis disorder 1A (Zellweger)|Zellweger spectrum disorders|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}