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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: 15-42142554-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=42142554&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 42142554,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_213600.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2303G>A",
"hgvs_p": "p.Arg768His",
"transcript": "NM_213600.4",
"protein_id": "NP_998765.3",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 849,
"cds_start": 2303,
"cds_end": null,
"cds_length": 2550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000397272.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_213600.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2303G>A",
"hgvs_p": "p.Arg768His",
"transcript": "ENST00000397272.7",
"protein_id": "ENSP00000380442.4",
"transcript_support_level": 1,
"aa_start": 768,
"aa_end": null,
"aa_length": 849,
"cds_start": 2303,
"cds_end": null,
"cds_length": 2550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_213600.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397272.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "n.*2047G>A",
"hgvs_p": null,
"transcript": "ENST00000290497.11",
"protein_id": "ENSP00000290497.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000290497.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "n.*108G>A",
"hgvs_p": null,
"transcript": "ENST00000562320.1",
"protein_id": "ENSP00000455037.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000562320.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "n.*1347G>A",
"hgvs_p": null,
"transcript": "ENST00000569985.5",
"protein_id": "ENSP00000454330.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000569985.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "n.*2047G>A",
"hgvs_p": null,
"transcript": "ENST00000290497.11",
"protein_id": "ENSP00000290497.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000290497.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "n.*108G>A",
"hgvs_p": null,
"transcript": "ENST00000562320.1",
"protein_id": "ENSP00000455037.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000562320.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "n.*1347G>A",
"hgvs_p": null,
"transcript": "ENST00000569985.5",
"protein_id": "ENSP00000454330.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000569985.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2429G>A",
"hgvs_p": "p.Arg810His",
"transcript": "ENST00000956233.1",
"protein_id": "ENSP00000626292.1",
"transcript_support_level": null,
"aa_start": 810,
"aa_end": null,
"aa_length": 891,
"cds_start": 2429,
"cds_end": null,
"cds_length": 2676,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956233.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2300G>A",
"hgvs_p": "p.Arg767His",
"transcript": "ENST00000888451.1",
"protein_id": "ENSP00000558510.1",
"transcript_support_level": null,
"aa_start": 767,
"aa_end": null,
"aa_length": 848,
"cds_start": 2300,
"cds_end": null,
"cds_length": 2547,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888451.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2300G>A",
"hgvs_p": "p.Arg767His",
"transcript": "ENST00000888452.1",
"protein_id": "ENSP00000558511.1",
"transcript_support_level": null,
"aa_start": 767,
"aa_end": null,
"aa_length": 848,
"cds_start": 2300,
"cds_end": null,
"cds_length": 2547,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888452.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2297G>A",
"hgvs_p": "p.Arg766His",
"transcript": "ENST00000888455.1",
"protein_id": "ENSP00000558514.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 847,
"cds_start": 2297,
"cds_end": null,
"cds_length": 2544,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888455.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2279G>A",
"hgvs_p": "p.Arg760His",
"transcript": "ENST00000888453.1",
"protein_id": "ENSP00000558512.1",
"transcript_support_level": null,
"aa_start": 760,
"aa_end": null,
"aa_length": 841,
"cds_start": 2279,
"cds_end": null,
"cds_length": 2526,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888453.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2273G>A",
"hgvs_p": "p.Arg758His",
"transcript": "ENST00000888454.1",
"protein_id": "ENSP00000558513.1",
"transcript_support_level": null,
"aa_start": 758,
"aa_end": null,
"aa_length": 839,
"cds_start": 2273,
"cds_end": null,
"cds_length": 2520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888454.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2234G>A",
"hgvs_p": "p.Arg745His",
"transcript": "ENST00000956234.1",
"protein_id": "ENSP00000626293.1",
"transcript_support_level": null,
"aa_start": 745,
"aa_end": null,
"aa_length": 826,
"cds_start": 2234,
"cds_end": null,
"cds_length": 2481,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956234.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "c.2102G>A",
"hgvs_p": "p.Arg701His",
"transcript": "ENST00000956235.1",
"protein_id": "ENSP00000626294.1",
"transcript_support_level": null,
"aa_start": 701,
"aa_end": null,
"aa_length": 782,
"cds_start": 2102,
"cds_end": null,
"cds_length": 2349,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956235.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "n.2317G>A",
"hgvs_p": null,
"transcript": "NR_033151.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033151.2"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"hgvs_c": "n.*72G>A",
"hgvs_p": null,
"transcript": "XR_931785.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_931785.1"
}
],
"gene_symbol": "PLA2G4F",
"gene_hgnc_id": 27396,
"dbsnp": "rs138996971",
"frequency_reference_population": 0.00006444904,
"hom_count_reference_population": 0,
"allele_count_reference_population": 104,
"gnomad_exomes_af": 0.0000595252,
"gnomad_genomes_af": 0.00011176,
"gnomad_exomes_ac": 87,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01953136920928955,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.047,
"revel_prediction": "Benign",
"alphamissense_score": 0.0711,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.859,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_213600.4",
"gene_symbol": "PLA2G4F",
"hgnc_id": 27396,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2303G>A",
"hgvs_p": "p.Arg768His"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}