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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: 16-88810550-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=88810550&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 88810550,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000485.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "NM_000485.3",
"protein_id": "NP_000476.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 180,
"cds_start": 194,
"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": "D",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "ENST00000378364.8",
"protein_id": "ENSP00000367615.3",
"transcript_support_level": 1,
"aa_start": 65,
"aa_end": null,
"aa_length": 180,
"cds_start": 194,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.440A>T",
"hgvs_p": "p.Asp147Val",
"transcript": "ENST00000912471.1",
"protein_id": "ENSP00000582530.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 262,
"cds_start": 440,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.287A>T",
"hgvs_p": "p.Asp96Val",
"transcript": "ENST00000880214.1",
"protein_id": "ENSP00000550273.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 211,
"cds_start": 287,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "ENST00000880215.1",
"protein_id": "ENSP00000550274.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 209,
"cds_start": 194,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "ENST00000912467.1",
"protein_id": "ENSP00000582526.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 179,
"cds_start": 194,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "ENST00000912468.1",
"protein_id": "ENSP00000582527.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 178,
"cds_start": 194,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.191A>T",
"hgvs_p": "p.Asp64Val",
"transcript": "ENST00000569616.1",
"protein_id": "ENSP00000455692.1",
"transcript_support_level": 5,
"aa_start": 64,
"aa_end": null,
"aa_length": 161,
"cds_start": 191,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "ENST00000567713.5",
"protein_id": "ENSP00000455749.1",
"transcript_support_level": 5,
"aa_start": 65,
"aa_end": null,
"aa_length": 147,
"cds_start": 194,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "NM_001030018.2",
"protein_id": "NP_001025189.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 134,
"cds_start": 194,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "ENST00000426324.6",
"protein_id": "ENSP00000397007.2",
"transcript_support_level": 2,
"aa_start": 65,
"aa_end": null,
"aa_length": 134,
"cds_start": 194,
"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": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.194A>T",
"hgvs_p": "p.Asp65Val",
"transcript": "ENST00000912470.1",
"protein_id": "ENSP00000582529.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 132,
"cds_start": 194,
"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": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.87A>T",
"hgvs_p": "p.Arg29Ser",
"transcript": "ENST00000912473.1",
"protein_id": "ENSP00000582532.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 118,
"cds_start": 87,
"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,
"aa_alt": null,
"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.241-402A>T",
"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,
"cds_end": null,
"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.81-402A>T",
"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.81-420A>T",
"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,
"cds_end": null,
"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.332-402A>T",
"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.188-402A>T",
"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,
"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": "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.188-402A>T",
"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,
"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": "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.-152A>T",
"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": "rs104894506",
"frequency_reference_population": 0.000007538708,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000753871,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9906407594680786,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.925,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.976,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.56,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.575,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000485.3",
"gene_symbol": "APRT",
"hgnc_id": 626,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.194A>T",
"hgvs_p": "p.Asp65Val"
}
],
"clinvar_disease": "Adenine phosphoribosyltransferase deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 O:1",
"phenotype_combined": "Adenine phosphoribosyltransferase deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}