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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: 19-5696253-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=5696253&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 5696253,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000360614.8",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1892C>A",
"hgvs_p": "p.Ser631Tyr",
"transcript": "NM_004793.4",
"protein_id": "NP_004784.2",
"transcript_support_level": null,
"aa_start": 631,
"aa_end": null,
"aa_length": 959,
"cds_start": 1892,
"cds_end": null,
"cds_length": 2880,
"cdna_start": 1906,
"cdna_end": null,
"cdna_length": 3092,
"mane_select": "ENST00000360614.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1892C>A",
"hgvs_p": "p.Ser631Tyr",
"transcript": "ENST00000360614.8",
"protein_id": "ENSP00000353826.2",
"transcript_support_level": 1,
"aa_start": 631,
"aa_end": null,
"aa_length": 959,
"cds_start": 1892,
"cds_end": null,
"cds_length": 2880,
"cdna_start": 1906,
"cdna_end": null,
"cdna_length": 3092,
"mane_select": "NM_004793.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1502C>A",
"hgvs_p": "p.Ser501Tyr",
"transcript": "ENST00000590729.5",
"protein_id": "ENSP00000465139.1",
"transcript_support_level": 1,
"aa_start": 501,
"aa_end": null,
"aa_length": 829,
"cds_start": 1502,
"cds_end": null,
"cds_length": 2490,
"cdna_start": 1561,
"cdna_end": null,
"cdna_length": 2626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1700C>A",
"hgvs_p": "p.Ser567Tyr",
"transcript": "NM_001276479.2",
"protein_id": "NP_001263408.1",
"transcript_support_level": null,
"aa_start": 567,
"aa_end": null,
"aa_length": 895,
"cds_start": 1700,
"cds_end": null,
"cds_length": 2688,
"cdna_start": 1714,
"cdna_end": null,
"cdna_length": 2900,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1700C>A",
"hgvs_p": "p.Ser567Tyr",
"transcript": "ENST00000593119.5",
"protein_id": "ENSP00000468541.1",
"transcript_support_level": 2,
"aa_start": 567,
"aa_end": null,
"aa_length": 895,
"cds_start": 1700,
"cds_end": null,
"cds_length": 2688,
"cdna_start": 1733,
"cdna_end": null,
"cdna_length": 2918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1550C>A",
"hgvs_p": "p.Ser517Tyr",
"transcript": "ENST00000585374.5",
"protein_id": "ENSP00000465585.1",
"transcript_support_level": 5,
"aa_start": 517,
"aa_end": null,
"aa_length": 845,
"cds_start": 1550,
"cds_end": null,
"cds_length": 2538,
"cdna_start": 1697,
"cdna_end": null,
"cdna_length": 2882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1304C>A",
"hgvs_p": "p.Ser435Tyr",
"transcript": "NM_001276480.1",
"protein_id": "NP_001263409.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 763,
"cds_start": 1304,
"cds_end": null,
"cds_length": 2292,
"cdna_start": 1697,
"cdna_end": null,
"cdna_length": 2883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "c.1304C>A",
"hgvs_p": "p.Ser435Tyr",
"transcript": "ENST00000540670.6",
"protein_id": "ENSP00000441523.1",
"transcript_support_level": 2,
"aa_start": 435,
"aa_end": null,
"aa_length": 763,
"cds_start": 1304,
"cds_end": null,
"cds_length": 2292,
"cdna_start": 1817,
"cdna_end": null,
"cdna_length": 3002,
"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": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "n.1630C>A",
"hgvs_p": null,
"transcript": "ENST00000587552.5",
"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": 2816,
"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": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "n.*1141C>A",
"hgvs_p": null,
"transcript": "ENST00000590558.5",
"protein_id": "ENSP00000467808.1",
"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": 2884,
"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": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "n.1697C>A",
"hgvs_p": null,
"transcript": "NR_076392.2",
"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": 2883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"hgvs_c": "n.*1141C>A",
"hgvs_p": null,
"transcript": "ENST00000590558.5",
"protein_id": "ENSP00000467808.1",
"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": 2884,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LONP1",
"gene_hgnc_id": 9479,
"dbsnp": "rs879255248",
"frequency_reference_population": 0.000010951733,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.0000109517,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9775570631027222,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.988,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.943,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.53,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.274,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000360614.8",
"gene_symbol": "LONP1",
"hgnc_id": 9479,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,XL",
"hgvs_c": "c.1892C>A",
"hgvs_p": "p.Ser631Tyr"
}
],
"clinvar_disease": "CODAS syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "CODAS syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}