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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: 14-31599308-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=31599308&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 31599308,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000281081.12",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"transcript": "NM_025152.3",
"protein_id": "NP_079428.2",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 319,
"cds_start": 311,
"cds_end": null,
"cds_length": 960,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 3040,
"mane_select": "ENST00000281081.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"transcript": "ENST00000281081.12",
"protein_id": "ENSP00000281081.7",
"transcript_support_level": 1,
"aa_start": 104,
"aa_end": null,
"aa_length": 319,
"cds_start": 311,
"cds_end": null,
"cds_length": 960,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 3040,
"mane_select": "NM_025152.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.23T>C",
"hgvs_p": "p.Leu8Pro",
"transcript": "NM_001201573.2",
"protein_id": "NP_001188502.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 223,
"cds_start": 23,
"cds_end": null,
"cds_length": 672,
"cdna_start": 130,
"cdna_end": null,
"cdna_length": 2823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.155T>C",
"hgvs_p": "p.Leu52Pro",
"transcript": "ENST00000551314.1",
"protein_id": "ENSP00000447234.1",
"transcript_support_level": 4,
"aa_start": 52,
"aa_end": null,
"aa_length": 132,
"cds_start": 155,
"cds_end": null,
"cds_length": 400,
"cdna_start": 322,
"cdna_end": null,
"cdna_length": 567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"transcript": "XM_017021664.2",
"protein_id": "XP_016877153.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 197,
"cds_start": 311,
"cds_end": null,
"cds_length": 594,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 13340,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"transcript": "XM_017021665.3",
"protein_id": "XP_016877154.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 185,
"cds_start": 311,
"cds_end": null,
"cds_length": 558,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 4569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"transcript": "XM_011537183.3",
"protein_id": "XP_011535485.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 181,
"cds_start": 311,
"cds_end": null,
"cds_length": 546,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 2314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"transcript": "XM_017021666.2",
"protein_id": "XP_016877155.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 181,
"cds_start": 311,
"cds_end": null,
"cds_length": 546,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 2260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"transcript": "XM_047431788.1",
"protein_id": "XP_047287744.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 173,
"cds_start": 311,
"cds_end": null,
"cds_length": 522,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"transcript": "XM_047431789.1",
"protein_id": "XP_047287745.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 165,
"cds_start": 311,
"cds_end": null,
"cds_length": 498,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.36T>C",
"hgvs_p": "p.Ala12Ala",
"transcript": "XM_011537181.3",
"protein_id": "XP_011535483.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 214,
"cds_start": 36,
"cds_end": null,
"cds_length": 645,
"cdna_start": 130,
"cdna_end": null,
"cdna_length": 2783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "n.311T>C",
"hgvs_p": null,
"transcript": "ENST00000547839.5",
"protein_id": "ENSP00000449918.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "n.315T>C",
"hgvs_p": null,
"transcript": "ENST00000548937.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "n.275T>C",
"hgvs_p": null,
"transcript": "ENST00000549838.5",
"protein_id": "ENSP00000447658.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "n.260T>C",
"hgvs_p": null,
"transcript": "ENST00000550355.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "n.*93T>C",
"hgvs_p": null,
"transcript": "ENST00000552489.5",
"protein_id": "ENSP00000447316.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "n.347T>C",
"hgvs_p": null,
"transcript": "NR_120408.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2946,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "n.347T>C",
"hgvs_p": null,
"transcript": "XR_007064050.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.-73T>C",
"hgvs_p": null,
"transcript": "XM_047431787.1",
"protein_id": "XP_047287743.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 178,
"cds_start": -4,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "n.*93T>C",
"hgvs_p": null,
"transcript": "ENST00000552489.5",
"protein_id": "ENSP00000447316.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.291+34260T>C",
"hgvs_p": null,
"transcript": "ENST00000550649.5",
"protein_id": "ENSP00000447618.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 166,
"cds_start": -4,
"cds_end": null,
"cds_length": 502,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"hgvs_c": "c.-145T>C",
"hgvs_p": null,
"transcript": "XM_047431786.1",
"protein_id": "XP_047287742.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 189,
"cds_start": -4,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2736,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NUBPL",
"gene_hgnc_id": 20278,
"dbsnp": "rs201430951",
"frequency_reference_population": 0.0001960249,
"hom_count_reference_population": 0,
"allele_count_reference_population": 316,
"gnomad_exomes_af": 0.000211666,
"gnomad_genomes_af": 0.0000459933,
"gnomad_exomes_ac": 309,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8456642627716064,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.759,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9946,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.55,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000281081.12",
"gene_symbol": "NUBPL",
"hgnc_id": 20278,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro"
}
],
"clinvar_disease": " nuclear type 21,Inborn genetic diseases,Mitochondrial complex I deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:1",
"phenotype_combined": "Mitochondrial complex I deficiency|Inborn genetic diseases|not provided|Mitochondrial complex I deficiency, nuclear type 21",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}