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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: 16-46689730-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=46689730&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ORC6",
"hgnc_id": 17151,
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_014321.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "VPS35",
"hgnc_id": 13487,
"hgvs_c": "n.-212G>T",
"hgvs_p": null,
"inheritance_mode": "AD,AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000569950.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": 0.1118,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"chr": "16",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.23535293340682983,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 252,
"aa_ref": "L",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1615,
"cdna_start": 72,
"cds_end": null,
"cds_length": 759,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_014321.4",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000219097.7",
"protein_coding": true,
"protein_id": "NP_055136.1",
"strand": true,
"transcript": "NM_014321.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 252,
"aa_ref": "L",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1615,
"cdna_start": 72,
"cds_end": null,
"cds_length": 759,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000219097.7",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014321.4",
"protein_coding": true,
"protein_id": "ENSP00000219097.2",
"strand": true,
"transcript": "ENST00000219097.7",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 283,
"aa_ref": "L",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1945,
"cdna_start": 311,
"cds_end": null,
"cds_length": 852,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000912416.1",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582475.1",
"strand": true,
"transcript": "ENST00000912416.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 251,
"aa_ref": "L",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1663,
"cdna_start": 123,
"cds_end": null,
"cds_length": 756,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000912417.1",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582476.1",
"strand": true,
"transcript": "ENST00000912417.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 230,
"aa_ref": "L",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1535,
"cdna_start": 58,
"cds_end": null,
"cds_length": 693,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000912418.1",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582477.1",
"strand": true,
"transcript": "ENST00000912418.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 229,
"aa_ref": "L",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1811,
"cdna_start": 337,
"cds_end": null,
"cds_length": 690,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000912415.1",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582474.1",
"strand": true,
"transcript": "ENST00000912415.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 222,
"aa_ref": "L",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1499,
"cdna_start": 46,
"cds_end": null,
"cds_length": 669,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000942255.1",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612314.1",
"strand": true,
"transcript": "ENST00000942255.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 167,
"aa_ref": "L",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 888,
"cdna_start": 34,
"cds_end": null,
"cds_length": 504,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000568364.6",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000457282.2",
"strand": true,
"transcript": "ENST00000568364.6",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 192,
"aa_ref": "L",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 718,
"cdna_start": 72,
"cds_end": null,
"cds_length": 579,
"cds_start": 25,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_011522978.4",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "c.25C>A",
"hgvs_p": "p.Leu9Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011521280.1",
"strand": true,
"transcript": "XM_011522978.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1190,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000563306.5",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "n.49C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000563306.5",
"transcript_support_level": 2
},
{
"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": 681,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000563599.5",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "n.25C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000454299.1",
"strand": true,
"transcript": "ENST00000563599.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1833,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000569239.5",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "n.72C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000569239.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 561,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000570260.2",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "n.24C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000570260.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1674,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NR_037620.2",
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"hgvs_c": "n.72C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_037620.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1096,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000569950.1",
"gene_hgnc_id": 13487,
"gene_symbol": "VPS35",
"hgvs_c": "n.-212G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000569950.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1329167923",
"effect": "missense_variant",
"frequency_reference_population": 0.0000013789129,
"gene_hgnc_id": 17151,
"gene_symbol": "ORC6",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000137891,
"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": "Inborn genetic diseases",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.794,
"pos": 46689730,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.085,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_014321.4"
}
]
}