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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: 2-73950574-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=73950574&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3",
"PP5"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DGUOK",
"hgnc_id": 2858,
"hgvs_c": "c.444-11C>G",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 8,
"score": 8,
"transcript": "NM_080916.3",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3",
"PP5"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DGUOK-AS1",
"hgnc_id": 43441,
"hgvs_c": "n.308-2639G>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 8,
"score": 8,
"transcript": "ENST00000453103.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PS3,PM2,PP3,PP5",
"acmg_score": 8,
"allele_count_reference_population": 9,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.8,
"chr": "2",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " autosomal recessive 4,Progressive external ophthalmoplegia with mitochondrial DNA deletions,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:1 US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.800000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 277,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1075,
"cdna_start": null,
"cds_end": null,
"cds_length": 834,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_080916.3",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.444-11C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264093.9",
"protein_coding": true,
"protein_id": "NP_550438.1",
"strand": true,
"transcript": "NM_080916.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 277,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1075,
"cdna_start": null,
"cds_end": null,
"cds_length": 834,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000264093.9",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.444-11C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_080916.3",
"protein_coding": true,
"protein_id": "ENSP00000264093.4",
"strand": true,
"transcript": "ENST00000264093.9",
"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": 703,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000418996.5",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "n.*60+3668C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000408209.1",
"strand": true,
"transcript": "ENST00000418996.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 271,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1158,
"cdna_start": null,
"cds_end": null,
"cds_length": 816,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000893377.1",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.426-11C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563436.1",
"strand": true,
"transcript": "ENST00000893377.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 263,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1041,
"cdna_start": null,
"cds_end": null,
"cds_length": 792,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000893380.1",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.444-53C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563439.1",
"strand": true,
"transcript": "ENST00000893380.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 189,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 811,
"cdna_start": null,
"cds_end": null,
"cds_length": 570,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_080918.3",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.443+3668C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_550440.1",
"strand": true,
"transcript": "NM_080918.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 189,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 880,
"cdna_start": null,
"cds_end": null,
"cds_length": 570,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000348222.3",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.443+3668C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000306964.3",
"strand": true,
"transcript": "ENST00000348222.3",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 183,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 793,
"cdna_start": null,
"cds_end": null,
"cds_length": 552,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001318859.2",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.425+3686C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305788.1",
"strand": true,
"transcript": "NM_001318859.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 183,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 851,
"cdna_start": null,
"cds_end": null,
"cds_length": 552,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000893378.1",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.425+3686C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563437.1",
"strand": true,
"transcript": "ENST00000893378.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 180,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 962,
"cdna_start": null,
"cds_end": null,
"cds_length": 543,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001318860.2",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.153-11C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305789.1",
"strand": true,
"transcript": "NM_001318860.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 180,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1048,
"cdna_start": null,
"cds_end": null,
"cds_length": 543,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001318861.2",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.153-11C>G",
"hgvs_p": null,
"intron_rank": 3,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_001305790.1",
"strand": true,
"transcript": "NM_001318861.2",
"transcript_support_level": null
},
{
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"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1030,
"cdna_start": null,
"cds_end": null,
"cds_length": 525,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
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"feature": "NM_001318862.2",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.135-11C>G",
"hgvs_p": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_001305791.1",
"strand": true,
"transcript": "NM_001318862.2",
"transcript_support_level": null
},
{
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"cdna_start": null,
"cds_end": null,
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"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
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"feature": "NM_001318863.2",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.135-11C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305792.1",
"strand": true,
"transcript": "NM_001318863.2",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
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"cdna_end": null,
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"cdna_start": null,
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"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
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"feature": "ENST00000893379.1",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.256-6551C>G",
"hgvs_p": null,
"intron_rank": 2,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000563438.1",
"strand": true,
"transcript": "ENST00000893379.1",
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},
{
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
"cds_length": 417,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000893381.1",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.143-11C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563440.1",
"strand": true,
"transcript": "ENST00000893381.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 616,
"cdna_start": null,
"cds_end": null,
"cds_length": 375,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000915418.1",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.143-53C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585477.1",
"strand": true,
"transcript": "ENST00000915418.1",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"cds_start": null,
"consequences": [
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],
"exon_count": 4,
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"feature": "ENST00000915416.1",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.134-6597C>G",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000585475.1",
"strand": true,
"transcript": "ENST00000915416.1",
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},
{
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"consequences": [
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],
"exon_count": 3,
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"feature": "ENST00000915417.1",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.143-7526C>G",
"hgvs_p": null,
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"intron_rank_end": null,
"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000585476.1",
"strand": true,
"transcript": "ENST00000915417.1",
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},
{
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"consequences": [
"intron_variant"
],
"exon_count": 7,
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"feature": "XM_011532647.3",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.426-11C>G",
"hgvs_p": null,
"intron_rank": 3,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530949.1",
"strand": true,
"transcript": "XM_011532647.3",
"transcript_support_level": null
},
{
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"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 723,
"cdna_start": null,
"cds_end": null,
"cds_length": 603,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047443585.1",
"gene_hgnc_id": 2858,
"gene_symbol": "DGUOK",
"hgvs_c": "c.444-11C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299541.1",
"strand": true,
"transcript": "XM_047443585.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 739,
"cdna_start": null,
"cds_end": null,
"cds_length": 498,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047443587.1",
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"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328282,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 4|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.649,
"pos": 73950574,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9860000014305115,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.7,
"transcript": "NM_080916.3"
}
]
}