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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: 3-132671032-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=132671032&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 132671032,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000356232.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Arg188*",
"transcript": "NM_024818.6",
"protein_id": "NP_079094.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 404,
"cds_start": 562,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 771,
"cdna_end": null,
"cdna_length": 4692,
"mane_select": "ENST00000356232.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Arg188*",
"transcript": "ENST00000356232.10",
"protein_id": "ENSP00000348565.4",
"transcript_support_level": 1,
"aa_start": 188,
"aa_end": null,
"aa_length": 404,
"cds_start": 562,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 771,
"cdna_end": null,
"cdna_length": 4692,
"mane_select": "NM_024818.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.394C>T",
"hgvs_p": "p.Arg132*",
"transcript": "ENST00000494238.6",
"protein_id": "ENSP00000418807.2",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 348,
"cds_start": 394,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 1088,
"cdna_end": null,
"cdna_length": 2997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "c.635+10882G>A",
"hgvs_p": null,
"transcript": "ENST00000632629.1",
"protein_id": "ENSP00000488520.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 230,
"cds_start": -4,
"cds_end": null,
"cds_length": 694,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 695,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.733C>T",
"hgvs_p": "p.Arg245*",
"transcript": "ENST00000683741.1",
"protein_id": "ENSP00000507396.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 461,
"cds_start": 733,
"cds_end": null,
"cds_length": 1386,
"cdna_start": 733,
"cdna_end": null,
"cdna_length": 4575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Arg188*",
"transcript": "ENST00000493720.6",
"protein_id": "ENSP00000417879.2",
"transcript_support_level": 5,
"aa_start": 188,
"aa_end": null,
"aa_length": 377,
"cds_start": 562,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 1154,
"cdna_end": null,
"cdna_length": 2058,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.394C>T",
"hgvs_p": "p.Arg132*",
"transcript": "NM_001320210.2",
"protein_id": "NP_001307139.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 348,
"cds_start": 394,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 1121,
"cdna_end": null,
"cdna_length": 5042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.394C>T",
"hgvs_p": "p.Arg132*",
"transcript": "NM_198329.4",
"protein_id": "NP_938143.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 348,
"cds_start": 394,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 642,
"cdna_end": null,
"cdna_length": 4563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.394C>T",
"hgvs_p": "p.Arg132*",
"transcript": "ENST00000264991.8",
"protein_id": "ENSP00000264991.4",
"transcript_support_level": 5,
"aa_start": 132,
"aa_end": null,
"aa_length": 348,
"cds_start": 394,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 2850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Arg188*",
"transcript": "ENST00000473651.5",
"protein_id": "ENSP00000424984.1",
"transcript_support_level": 5,
"aa_start": 188,
"aa_end": null,
"aa_length": 347,
"cds_start": 562,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 740,
"cdna_end": null,
"cdna_length": 1513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.292C>T",
"hgvs_p": "p.Arg98*",
"transcript": "NM_001321238.2",
"protein_id": "NP_001308167.1",
"transcript_support_level": null,
"aa_start": 98,
"aa_end": null,
"aa_length": 314,
"cds_start": 292,
"cds_end": null,
"cds_length": 945,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 4906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.226C>T",
"hgvs_p": "p.Arg76*",
"transcript": "NM_001321239.1",
"protein_id": "NP_001308168.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 292,
"cds_start": 226,
"cds_end": null,
"cds_length": 879,
"cdna_start": 1467,
"cdna_end": null,
"cdna_length": 3701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "c.292C>T",
"hgvs_p": "p.Arg98*",
"transcript": "ENST00000464068.5",
"protein_id": "ENSP00000420055.1",
"transcript_support_level": 5,
"aa_start": 98,
"aa_end": null,
"aa_length": 109,
"cds_start": 292,
"cds_end": null,
"cds_length": 332,
"cdna_start": 617,
"cdna_end": null,
"cdna_length": 657,
"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": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "n.1825C>T",
"hgvs_p": null,
"transcript": "ENST00000468227.5",
"protein_id": null,
"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": 3902,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "n.351C>T",
"hgvs_p": null,
"transcript": "ENST00000469158.1",
"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": 584,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "n.*231C>T",
"hgvs_p": null,
"transcript": "ENST00000505777.5",
"protein_id": "ENSP00000427233.1",
"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": 576,
"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": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "n.1603C>T",
"hgvs_p": null,
"transcript": "XR_007095728.1",
"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": 1969,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"hgvs_c": "n.*231C>T",
"hgvs_p": null,
"transcript": "ENST00000505777.5",
"protein_id": "ENSP00000427233.1",
"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": 576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 45,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.*1980+10882G>A",
"hgvs_p": null,
"transcript": "ENST00000471702.2",
"protein_id": "ENSP00000419763.1",
"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": 7784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 45,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.3995+10882G>A",
"hgvs_p": null,
"transcript": "NR_037804.1",
"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": 7788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "UBA5",
"gene_hgnc_id": 23230,
"dbsnp": "rs374052333",
"frequency_reference_population": 0.000024643861,
"hom_count_reference_population": 0,
"allele_count_reference_population": 36,
"gnomad_exomes_af": 0.0000246439,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 36,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6499999761581421,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.65,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.804,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000356232.10",
"gene_symbol": "UBA5",
"hgnc_id": 23230,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Arg188*"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000632629.1",
"gene_symbol": "NPHP3-ACAD11",
"hgnc_id": 48351,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.635+10882G>A",
"hgvs_p": null
}
],
"clinvar_disease": " 44, autosomal recessive 24,Developmental and epileptic encephalopathy,Spinocerebellar ataxia,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1",
"phenotype_combined": "Developmental and epileptic encephalopathy, 44|Developmental and epileptic encephalopathy, 44;Spinocerebellar ataxia, autosomal recessive 24|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}