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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: 16-88810482-T-TTCGG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=88810482&ref=T&alt=TTCGG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 88810482,
"ref": "T",
"alt": "TTCGG",
"effect": "frameshift_variant",
"transcript": "NM_000485.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs",
"transcript": "NM_000485.3",
"protein_id": "NP_000476.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 180,
"cds_start": 261,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000378364.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000485.3"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs",
"transcript": "ENST00000378364.8",
"protein_id": "ENSP00000367615.3",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 180,
"cds_start": 261,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000485.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378364.8"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.504_507dupCCGA",
"hgvs_p": "p.Lys170fs",
"transcript": "ENST00000912471.1",
"protein_id": "ENSP00000582530.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 262,
"cds_start": 507,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912471.1"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.351_354dupCCGA",
"hgvs_p": "p.Lys119fs",
"transcript": "ENST00000880214.1",
"protein_id": "ENSP00000550273.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 211,
"cds_start": 354,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880214.1"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs",
"transcript": "ENST00000880215.1",
"protein_id": "ENSP00000550274.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 209,
"cds_start": 261,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880215.1"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs",
"transcript": "ENST00000912467.1",
"protein_id": "ENSP00000582526.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 179,
"cds_start": 261,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912467.1"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs",
"transcript": "ENST00000912468.1",
"protein_id": "ENSP00000582527.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 178,
"cds_start": 261,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912468.1"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.255_258dupCCGA",
"hgvs_p": "p.Lys87fs",
"transcript": "ENST00000569616.1",
"protein_id": "ENSP00000455692.1",
"transcript_support_level": 5,
"aa_start": 86,
"aa_end": null,
"aa_length": 161,
"cds_start": 258,
"cds_end": null,
"cds_length": 486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000569616.1"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs",
"transcript": "ENST00000567713.5",
"protein_id": "ENSP00000455749.1",
"transcript_support_level": 5,
"aa_start": 87,
"aa_end": null,
"aa_length": 147,
"cds_start": 261,
"cds_end": null,
"cds_length": 446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000567713.5"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs",
"transcript": "NM_001030018.2",
"protein_id": "NP_001025189.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 134,
"cds_start": 261,
"cds_end": null,
"cds_length": 405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001030018.2"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs",
"transcript": "ENST00000426324.6",
"protein_id": "ENSP00000397007.2",
"transcript_support_level": 2,
"aa_start": 87,
"aa_end": null,
"aa_length": 134,
"cds_start": 261,
"cds_end": null,
"cds_length": 405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000426324.6"
},
{
"aa_ref": "R",
"aa_alt": "RP?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs",
"transcript": "ENST00000912470.1",
"protein_id": "ENSP00000582529.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 132,
"cds_start": 261,
"cds_end": null,
"cds_length": 399,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912470.1"
},
{
"aa_ref": "K",
"aa_alt": "TE?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.151_154dupCCGA",
"hgvs_p": "p.Lys52fs",
"transcript": "ENST00000912473.1",
"protein_id": "ENSP00000582532.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 118,
"cds_start": 154,
"cds_end": null,
"cds_length": 357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912473.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.241-338_241-335dupCCGA",
"hgvs_p": null,
"transcript": "ENST00000563655.5",
"protein_id": "ENSP00000456012.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": null,
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"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000563655.5"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.81-338_81-335dupCCGA",
"hgvs_p": null,
"transcript": "ENST00000912469.1",
"protein_id": "ENSP00000582528.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 55,
"cds_start": null,
"cds_end": null,
"cds_length": 168,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912469.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "c.81-356_81-353dupCCGA",
"hgvs_p": null,
"transcript": "ENST00000912472.1",
"protein_id": "ENSP00000582531.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 49,
"cds_start": null,
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"cds_length": 150,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912472.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "n.332-338_332-335dupCCGA",
"hgvs_p": null,
"transcript": "ENST00000562464.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000562464.1"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "n.188-338_188-335dupCCGA",
"hgvs_p": null,
"transcript": "ENST00000567391.5",
"protein_id": "ENSP00000457964.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
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"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000567391.5"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "n.188-338_188-335dupCCGA",
"hgvs_p": null,
"transcript": "ENST00000568319.5",
"protein_id": "ENSP00000456905.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
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"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000568319.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "n.-218_-215dupCCGA",
"hgvs_p": null,
"transcript": "ENST00000567057.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000567057.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"hgvs_c": "n.-88_-85dupCCGA",
"hgvs_p": null,
"transcript": "ENST00000568575.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000568575.1"
}
],
"gene_symbol": "APRT",
"gene_hgnc_id": 626,
"dbsnp": "rs281860265",
"frequency_reference_population": 6.8490993e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8491e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -2.482,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_000485.3",
"gene_symbol": "APRT",
"hgnc_id": 626,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.258_261dupCCGA",
"hgvs_p": "p.Lys88fs"
}
],
"clinvar_disease": "Adenine phosphoribosyltransferase deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Adenine phosphoribosyltransferase deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}