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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: 15-42142003-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=42142003&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PLA2G4F",
"hgnc_id": 27396,
"hgvs_c": "c.2531G>C",
"hgvs_p": "p.Arg844Pro",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_213600.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 4,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1139,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.58,
"chr": "15",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.06635311245918274,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 849,
"aa_ref": "R",
"aa_start": 844,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5587,
"cdna_start": 2618,
"cds_end": null,
"cds_length": 2550,
"cds_start": 2531,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_213600.4",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2531G>C",
"hgvs_p": "p.Arg844Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000397272.7",
"protein_coding": true,
"protein_id": "NP_998765.3",
"strand": false,
"transcript": "NM_213600.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 849,
"aa_ref": "R",
"aa_start": 844,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5587,
"cdna_start": 2618,
"cds_end": null,
"cds_length": 2550,
"cds_start": 2531,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000397272.7",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2531G>C",
"hgvs_p": "p.Arg844Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_213600.4",
"protein_coding": true,
"protein_id": "ENSP00000380442.4",
"strand": false,
"transcript": "ENST00000397272.7",
"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": 3319,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000290497.11",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "n.*2275G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000290497.7",
"strand": false,
"transcript": "ENST00000290497.11",
"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": 1402,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000562320.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "n.*336G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000455037.1",
"strand": false,
"transcript": "ENST00000562320.1",
"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": 3329,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000569985.5",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "n.*1575G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000454330.1",
"strand": false,
"transcript": "ENST00000569985.5",
"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": 3319,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000290497.11",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "n.*2275G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000290497.7",
"strand": false,
"transcript": "ENST00000290497.11",
"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": 1402,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000562320.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "n.*336G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000455037.1",
"strand": false,
"transcript": "ENST00000562320.1",
"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": 3329,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000569985.5",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "n.*1575G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000454330.1",
"strand": false,
"transcript": "ENST00000569985.5",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 891,
"aa_ref": "R",
"aa_start": 886,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3509,
"cdna_start": 2712,
"cds_end": null,
"cds_length": 2676,
"cds_start": 2657,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000956233.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2657G>C",
"hgvs_p": "p.Arg886Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626292.1",
"strand": false,
"transcript": "ENST00000956233.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 848,
"aa_ref": "R",
"aa_start": 843,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4398,
"cdna_start": 2575,
"cds_end": null,
"cds_length": 2547,
"cds_start": 2528,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000888451.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2528G>C",
"hgvs_p": "p.Arg843Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558510.1",
"strand": false,
"transcript": "ENST00000888451.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 848,
"aa_ref": "R",
"aa_start": 843,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3437,
"cdna_start": 2638,
"cds_end": null,
"cds_length": 2547,
"cds_start": 2528,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000888452.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2528G>C",
"hgvs_p": "p.Arg843Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558511.1",
"strand": false,
"transcript": "ENST00000888452.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 847,
"aa_ref": "R",
"aa_start": 842,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3375,
"cdna_start": 2585,
"cds_end": null,
"cds_length": 2544,
"cds_start": 2525,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000888455.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2525G>C",
"hgvs_p": "p.Arg842Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558514.1",
"strand": false,
"transcript": "ENST00000888455.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 841,
"aa_ref": "R",
"aa_start": 836,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3382,
"cdna_start": 2584,
"cds_end": null,
"cds_length": 2526,
"cds_start": 2507,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000888453.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2507G>C",
"hgvs_p": "p.Arg836Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558512.1",
"strand": false,
"transcript": "ENST00000888453.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 839,
"aa_ref": "R",
"aa_start": 834,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3355,
"cdna_start": 2556,
"cds_end": null,
"cds_length": 2520,
"cds_start": 2501,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000888454.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2501G>C",
"hgvs_p": "p.Arg834Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558513.1",
"strand": false,
"transcript": "ENST00000888454.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 826,
"aa_ref": "R",
"aa_start": 821,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3314,
"cdna_start": 2517,
"cds_end": null,
"cds_length": 2481,
"cds_start": 2462,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000956234.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2462G>C",
"hgvs_p": "p.Arg821Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626293.1",
"strand": false,
"transcript": "ENST00000956234.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 782,
"aa_ref": "R",
"aa_start": 777,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3170,
"cdna_start": 2377,
"cds_end": null,
"cds_length": 2349,
"cds_start": 2330,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000956235.1",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "c.2330G>C",
"hgvs_p": "p.Arg777Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626294.1",
"strand": false,
"transcript": "ENST00000956235.1",
"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": 5514,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NR_033151.2",
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"hgvs_c": "n.2545G>C",
"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_033151.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs372512124",
"effect": "missense_variant",
"frequency_reference_population": 0.000002736768,
"gene_hgnc_id": 27396,
"gene_symbol": "PLA2G4F",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000273677,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.065,
"pos": 42142003,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.029,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_213600.4"
}
]
}