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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: 3-98580709-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=98580709&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 98580709,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000097.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Cys",
"transcript": "NM_000097.7",
"protein_id": "NP_000088.3",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 454,
"cds_start": 1339,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000647941.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000097.7"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Cys",
"transcript": "ENST00000647941.2",
"protein_id": "ENSP00000497326.1",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 454,
"cds_start": 1339,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000097.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000647941.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285635",
"gene_hgnc_id": null,
"hgvs_c": "n.161+698C>T",
"hgvs_p": null,
"transcript": "ENST00000512905.6",
"protein_id": "ENSP00000425880.1",
"transcript_support_level": 5,
"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": "ENST00000512905.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"hgvs_c": "c.1426C>T",
"hgvs_p": "p.Arg476Cys",
"transcript": "ENST00000946176.1",
"protein_id": "ENSP00000616235.1",
"transcript_support_level": null,
"aa_start": 476,
"aa_end": null,
"aa_length": 483,
"cds_start": 1426,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946176.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"hgvs_c": "c.1336C>T",
"hgvs_p": "p.Arg446Cys",
"transcript": "ENST00000932270.1",
"protein_id": "ENSP00000602329.1",
"transcript_support_level": null,
"aa_start": 446,
"aa_end": null,
"aa_length": 453,
"cds_start": 1336,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932270.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"hgvs_c": "c.1234C>T",
"hgvs_p": "p.Arg412Cys",
"transcript": "ENST00000890710.1",
"protein_id": "ENSP00000560769.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 419,
"cds_start": 1234,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890710.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"hgvs_c": "c.1228C>T",
"hgvs_p": "p.Arg410Cys",
"transcript": "ENST00000890711.1",
"protein_id": "ENSP00000560770.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 417,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890711.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"hgvs_c": "c.1174C>T",
"hgvs_p": "p.Arg392Cys",
"transcript": "ENST00000890712.1",
"protein_id": "ENSP00000560771.1",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 399,
"cds_start": 1174,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890712.1"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"hgvs_c": "c.1173-2439C>T",
"hgvs_p": null,
"transcript": "XM_005247125.5",
"protein_id": "XP_005247182.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 405,
"cds_start": null,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247125.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"hgvs_c": "n.1280-2439C>T",
"hgvs_p": null,
"transcript": "XR_001740025.3",
"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_001740025.3"
}
],
"gene_symbol": "CPOX",
"gene_hgnc_id": 2321,
"dbsnp": "rs28931603",
"frequency_reference_population": 0.0003134738,
"hom_count_reference_population": 3,
"allele_count_reference_population": 506,
"gnomad_exomes_af": 0.000320144,
"gnomad_genomes_af": 0.000249458,
"gnomad_exomes_ac": 468,
"gnomad_genomes_ac": 38,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5640648007392883,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.856,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1186,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.178,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": "Likely_benign",
"acmg_criteria": "BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BS1_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_000097.7",
"gene_symbol": "CPOX",
"hgnc_id": 2321,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,SD,AD",
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Cys"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000512905.6",
"gene_symbol": "ENSG00000285635",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.161+698C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Coproporphyria,Hereditary coproporphyria,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:4",
"phenotype_combined": "Coproporphyria|Hereditary coproporphyria|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}