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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: 2-61048535-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=61048535&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 61048535,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_002618.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX13",
"gene_hgnc_id": 8855,
"hgvs_c": "c.977T>G",
"hgvs_p": "p.Ile326Arg",
"transcript": "NM_002618.4",
"protein_id": "NP_002609.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 403,
"cds_start": 977,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1017,
"cdna_end": null,
"cdna_length": 4472,
"mane_select": "ENST00000295030.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002618.4"
},
{
"aa_ref": "I",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX13",
"gene_hgnc_id": 8855,
"hgvs_c": "c.977T>G",
"hgvs_p": "p.Ile326Arg",
"transcript": "ENST00000295030.6",
"protein_id": "ENSP00000295030.4",
"transcript_support_level": 1,
"aa_start": 326,
"aa_end": null,
"aa_length": 403,
"cds_start": 977,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1017,
"cdna_end": null,
"cdna_length": 4472,
"mane_select": "NM_002618.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295030.6"
},
{
"aa_ref": "I",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX13",
"gene_hgnc_id": 8855,
"hgvs_c": "c.1076T>G",
"hgvs_p": "p.Ile359Arg",
"transcript": "ENST00000920043.1",
"protein_id": "ENSP00000590102.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 436,
"cds_start": 1076,
"cds_end": null,
"cds_length": 1311,
"cdna_start": 1285,
"cdna_end": null,
"cdna_length": 2007,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920043.1"
},
{
"aa_ref": "I",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX13",
"gene_hgnc_id": 8855,
"hgvs_c": "c.998T>G",
"hgvs_p": "p.Ile333Arg",
"transcript": "ENST00000902278.1",
"protein_id": "ENSP00000572337.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 410,
"cds_start": 998,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 1022,
"cdna_end": null,
"cdna_length": 1743,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902278.1"
},
{
"aa_ref": "I",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX13",
"gene_hgnc_id": 8855,
"hgvs_c": "c.851T>G",
"hgvs_p": "p.Ile284Arg",
"transcript": "ENST00000902277.1",
"protein_id": "ENSP00000572336.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 361,
"cds_start": 851,
"cds_end": null,
"cds_length": 1086,
"cdna_start": 910,
"cdna_end": null,
"cdna_length": 1630,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902277.1"
},
{
"aa_ref": "I",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX13",
"gene_hgnc_id": 8855,
"hgvs_c": "c.491T>G",
"hgvs_p": "p.Ile164Arg",
"transcript": "ENST00000971318.1",
"protein_id": "ENSP00000641377.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 241,
"cds_start": 491,
"cds_end": null,
"cds_length": 726,
"cdna_start": 518,
"cdna_end": null,
"cdna_length": 859,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971318.1"
},
{
"aa_ref": "I",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX13",
"gene_hgnc_id": 8855,
"hgvs_c": "c.437T>G",
"hgvs_p": "p.Ile146Arg",
"transcript": "ENST00000920044.1",
"protein_id": "ENSP00000590103.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 223,
"cds_start": 437,
"cds_end": null,
"cds_length": 672,
"cdna_start": 474,
"cdna_end": null,
"cdna_length": 865,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920044.1"
}
],
"gene_symbol": "PEX13",
"gene_hgnc_id": 8855,
"dbsnp": "rs61752115",
"frequency_reference_population": 6.840759e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84076e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9324249029159546,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.524,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9973,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.575,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_002618.4",
"gene_symbol": "PEX13",
"hgnc_id": 8855,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.977T>G",
"hgvs_p": "p.Ile326Arg"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}