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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: 7-92518165-GTTGATCAACCCAAA-TTGC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=92518165&ref=GTTGATCAACCCAAA&alt=TTGC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 92518165,
"ref": "GTTGATCAACCCAAA",
"alt": "TTGC",
"effect": "frameshift_variant,missense_variant",
"transcript": "ENST00000248633.9",
"consequences": [
{
"aa_ref": "VWVDQQ",
"aa_alt": "GK?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.434_448delTTTGGGTTGATCAACinsGCAA",
"hgvs_p": "p.Val145fs",
"transcript": "NM_000466.3",
"protein_id": "NP_000457.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 1283,
"cds_start": 434,
"cds_end": null,
"cds_length": 3852,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 4369,
"mane_select": "ENST00000248633.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VWVDQQ",
"aa_alt": "GK?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.434_448delTTTGGGTTGATCAACinsGCAA",
"hgvs_p": "p.Val145fs",
"transcript": "ENST00000248633.9",
"protein_id": "ENSP00000248633.4",
"transcript_support_level": 1,
"aa_start": 145,
"aa_end": null,
"aa_length": 1283,
"cds_start": 434,
"cds_end": null,
"cds_length": 3852,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 4369,
"mane_select": "NM_000466.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VWVDQQ",
"aa_alt": "GK?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.434_448delTTTGGGTTGATCAACinsGCAA",
"hgvs_p": "p.Val145fs",
"transcript": "ENST00000428214.5",
"protein_id": "ENSP00000394413.1",
"transcript_support_level": 1,
"aa_start": 145,
"aa_end": null,
"aa_length": 1226,
"cds_start": 434,
"cds_end": null,
"cds_length": 3681,
"cdna_start": 448,
"cdna_end": null,
"cdna_length": 3681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VWVDQQ",
"aa_alt": "GK?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.434_448delTTTGGGTTGATCAACinsGCAA",
"hgvs_p": "p.Val145fs",
"transcript": "NM_001282677.2",
"protein_id": "NP_001269606.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 1226,
"cds_start": 434,
"cds_end": null,
"cds_length": 3681,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 4198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VWVDQQ",
"aa_alt": "GK?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.434_448delTTTGGGTTGATCAACinsGCAA",
"hgvs_p": "p.Val145fs",
"transcript": "XM_047420472.1",
"protein_id": "XP_047276428.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 1227,
"cds_start": 434,
"cds_end": null,
"cds_length": 3684,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 3846,
"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": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "n.473_487delTTTGGGTTGATCAACinsGCAA",
"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": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.-191_-177delTTTGGGTTGATCAACinsGCAA",
"hgvs_p": null,
"transcript": "NM_001282678.2",
"protein_id": "NP_001269607.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1075,
"cds_start": -4,
"cds_end": null,
"cds_length": 3228,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4404,
"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": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"hgvs_c": "c.273+3923_273+3937delTTTGGGTTGATCAACinsGCAA",
"hgvs_p": null,
"transcript": "ENST00000438045.5",
"protein_id": "ENSP00000410438.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 961,
"cds_start": -4,
"cds_end": null,
"cds_length": 2886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3329,
"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.154-1477_154-1463delGTTGATCAACCCAAAinsTTGC",
"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
}
],
"gene_symbol": "PEX1",
"gene_hgnc_id": 8850,
"dbsnp": "rs62653598",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 7.943,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000248633.9",
"gene_symbol": "PEX1",
"hgnc_id": 8850,
"effects": [
"frameshift_variant",
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.434_448delTTTGGGTTGATCAACinsGCAA",
"hgvs_p": "p.Val145fs"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000746412.1",
"gene_symbol": "ENSG00000244055",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.154-1477_154-1463delGTTGATCAACCCAAAinsTTGC",
"hgvs_p": null
}
],
"clinvar_disease": "Heimler syndrome 1,Peroxisome biogenesis disorder 1A (Zellweger),Peroxisome biogenesis disorder 1B",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Heimler syndrome 1;Peroxisome biogenesis disorder 1B;Peroxisome biogenesis disorder 1A (Zellweger)",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}