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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: 15-28238721-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=28238721&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "HERC2",
"hgnc_id": 4868,
"hgvs_c": "c.3629T>C",
"hgvs_p": "p.Ile1210Thr",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_004667.6",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_score": 2,
"allele_count_reference_population": 69,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9897,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.38,
"chr": "15",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8511146306991577,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4834,
"aa_ref": "I",
"aa_start": 1210,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15364,
"cdna_start": 3765,
"cds_end": null,
"cds_length": 14505,
"cds_start": 3629,
"consequences": [
"missense_variant"
],
"exon_count": 93,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "NM_004667.6",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3629T>C",
"hgvs_p": "p.Ile1210Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000261609.13",
"protein_coding": true,
"protein_id": "NP_004658.3",
"strand": false,
"transcript": "NM_004667.6",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4834,
"aa_ref": "I",
"aa_start": 1210,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 15364,
"cdna_start": 3765,
"cds_end": null,
"cds_length": 14505,
"cds_start": 3629,
"consequences": [
"missense_variant"
],
"exon_count": 93,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000261609.13",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3629T>C",
"hgvs_p": "p.Ile1210Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004667.6",
"protein_coding": true,
"protein_id": "ENSP00000261609.8",
"strand": false,
"transcript": "ENST00000261609.13",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4829,
"aa_ref": "I",
"aa_start": 1205,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15349,
"cdna_start": 3750,
"cds_end": null,
"cds_length": 14490,
"cds_start": 3614,
"consequences": [
"missense_variant"
],
"exon_count": 93,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_006720726.4",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3614T>C",
"hgvs_p": "p.Ile1205Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006720789.1",
"strand": false,
"transcript": "XM_006720726.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4825,
"aa_ref": "I",
"aa_start": 1201,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15207,
"cdna_start": 3608,
"cds_end": null,
"cds_length": 14478,
"cds_start": 3602,
"consequences": [
"missense_variant"
],
"exon_count": 92,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_047433206.1",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3602T>C",
"hgvs_p": "p.Ile1201Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047289162.1",
"strand": false,
"transcript": "XM_047433206.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4796,
"aa_ref": "I",
"aa_start": 1172,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15476,
"cdna_start": 3877,
"cds_end": null,
"cds_length": 14391,
"cds_start": 3515,
"consequences": [
"missense_variant"
],
"exon_count": 92,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_005268276.6",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3515T>C",
"hgvs_p": "p.Ile1172Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005268333.1",
"strand": false,
"transcript": "XM_005268276.6",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4796,
"aa_ref": "I",
"aa_start": 1172,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15284,
"cdna_start": 3685,
"cds_end": null,
"cds_length": 14391,
"cds_start": 3515,
"consequences": [
"missense_variant"
],
"exon_count": 92,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_017022695.1",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3515T>C",
"hgvs_p": "p.Ile1172Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016878184.1",
"strand": false,
"transcript": "XM_017022695.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4796,
"aa_ref": "I",
"aa_start": 1172,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15181,
"cdna_start": 3582,
"cds_end": null,
"cds_length": 14391,
"cds_start": 3515,
"consequences": [
"missense_variant"
],
"exon_count": 92,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_017022696.2",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3515T>C",
"hgvs_p": "p.Ile1172Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016878185.1",
"strand": false,
"transcript": "XM_017022696.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4748,
"aa_ref": "I",
"aa_start": 1124,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15106,
"cdna_start": 3507,
"cds_end": null,
"cds_length": 14247,
"cds_start": 3371,
"consequences": [
"missense_variant"
],
"exon_count": 91,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_006720727.4",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3371T>C",
"hgvs_p": "p.Ile1124Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006720790.1",
"strand": false,
"transcript": "XM_006720727.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 4673,
"aa_ref": "I",
"aa_start": 1049,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14843,
"cdna_start": 3244,
"cds_end": null,
"cds_length": 14022,
"cds_start": 3146,
"consequences": [
"missense_variant"
],
"exon_count": 89,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_047433207.1",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3146T>C",
"hgvs_p": "p.Ile1049Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047289163.1",
"strand": false,
"transcript": "XM_047433207.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3084,
"aa_ref": "I",
"aa_start": 1210,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9531,
"cdna_start": 3765,
"cds_end": null,
"cds_length": 9255,
"cds_start": 3629,
"consequences": [
"missense_variant"
],
"exon_count": 61,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_047433208.1",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3629T>C",
"hgvs_p": "p.Ile1210Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047289164.1",
"strand": false,
"transcript": "XM_047433208.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2713,
"aa_ref": "I",
"aa_start": 1210,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8287,
"cdna_start": 3765,
"cds_end": null,
"cds_length": 8142,
"cds_start": 3629,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_047433209.1",
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"hgvs_c": "c.3629T>C",
"hgvs_p": "p.Ile1210Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047289165.1",
"strand": false,
"transcript": "XM_047433209.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs545686064",
"effect": "missense_variant",
"frequency_reference_population": 0.00004281502,
"gene_hgnc_id": 4868,
"gene_symbol": "HERC2",
"gnomad_exomes_ac": 62,
"gnomad_exomes_af": 0.0000424878,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 7,
"gnomad_genomes_af": 0.0000459498,
"gnomad_genomes_homalt": 0,
"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": "Inborn genetic diseases|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.325,
"pos": 28238721,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.93,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_004667.6"
}
]
}