← Back to variant description
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: 3-132675342-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=132675342&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PP3_Moderate",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "UBA5",
"hgnc_id": 23230,
"hgvs_c": "c.907T>C",
"hgvs_p": "p.Cys303Arg",
"inheritance_mode": "AR,AD",
"pathogenic_score": 11,
"score": 11,
"transcript": "NM_024818.6",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3_Moderate",
"PP5"
],
"effects": [
"intron_variant"
],
"gene_symbol": "NPHP3-ACAD11",
"hgnc_id": 48351,
"hgvs_c": "c.635+6572A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 9,
"score": 9,
"transcript": "ENST00000632629.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PP3_Moderate,PP5",
"acmg_score": 11,
"allele_count_reference_population": 4,
"alphamissense_prediction": null,
"alphamissense_score": 0.9987,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.22,
"chr": "3",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 44,Developmental and epileptic encephalopathy",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9142059087753296,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 404,
"aa_ref": "C",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4692,
"cdna_start": 1116,
"cds_end": null,
"cds_length": 1215,
"cds_start": 907,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_024818.6",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.907T>C",
"hgvs_p": "p.Cys303Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000356232.10",
"protein_coding": true,
"protein_id": "NP_079094.1",
"strand": true,
"transcript": "NM_024818.6",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 404,
"aa_ref": "C",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4692,
"cdna_start": 1116,
"cds_end": null,
"cds_length": 1215,
"cds_start": 907,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000356232.10",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.907T>C",
"hgvs_p": "p.Cys303Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024818.6",
"protein_coding": true,
"protein_id": "ENSP00000348565.4",
"strand": true,
"transcript": "ENST00000356232.10",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 348,
"aa_ref": "C",
"aa_start": 247,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2997,
"cdna_start": 1433,
"cds_end": null,
"cds_length": 1047,
"cds_start": 739,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000494238.6",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.739T>C",
"hgvs_p": "p.Cys247Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418807.2",
"strand": true,
"transcript": "ENST00000494238.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 230,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 695,
"cdna_start": null,
"cds_end": null,
"cds_length": 694,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000632629.1",
"gene_hgnc_id": 48351,
"gene_symbol": "NPHP3-ACAD11",
"hgvs_c": "c.635+6572A>G",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000488520.1",
"strand": false,
"transcript": "ENST00000632629.1",
"transcript_support_level": 2
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 461,
"aa_ref": "C",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4575,
"cdna_start": 1078,
"cds_end": null,
"cds_length": 1386,
"cds_start": 1078,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000683741.1",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.1078T>C",
"hgvs_p": "p.Cys360Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000507396.1",
"strand": true,
"transcript": "ENST00000683741.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 385,
"aa_ref": "C",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2618,
"cdna_start": 1059,
"cds_end": null,
"cds_length": 1158,
"cds_start": 850,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000967272.1",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.850T>C",
"hgvs_p": "p.Cys284Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637331.1",
"strand": true,
"transcript": "ENST00000967272.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 377,
"aa_ref": "C",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2058,
"cdna_start": 1499,
"cds_end": null,
"cds_length": 1134,
"cds_start": 907,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000493720.6",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.907T>C",
"hgvs_p": "p.Cys303Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000417879.2",
"strand": true,
"transcript": "ENST00000493720.6",
"transcript_support_level": 5
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 369,
"aa_ref": "C",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2568,
"cdna_start": 1011,
"cds_end": null,
"cds_length": 1110,
"cds_start": 802,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000967273.1",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.802T>C",
"hgvs_p": "p.Cys268Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637332.1",
"strand": true,
"transcript": "ENST00000967273.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 348,
"aa_ref": "C",
"aa_start": 247,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5042,
"cdna_start": 1466,
"cds_end": null,
"cds_length": 1047,
"cds_start": 739,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001320210.2",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.739T>C",
"hgvs_p": "p.Cys247Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001307139.1",
"strand": true,
"transcript": "NM_001320210.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 348,
"aa_ref": "C",
"aa_start": 247,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4563,
"cdna_start": 987,
"cds_end": null,
"cds_length": 1047,
"cds_start": 739,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_198329.4",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.739T>C",
"hgvs_p": "p.Cys247Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_938143.1",
"strand": true,
"transcript": "NM_198329.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 348,
"aa_ref": "C",
"aa_start": 247,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2850,
"cdna_start": 971,
"cds_end": null,
"cds_length": 1047,
"cds_start": 739,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000264991.8",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.739T>C",
"hgvs_p": "p.Cys247Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000264991.4",
"strand": true,
"transcript": "ENST00000264991.8",
"transcript_support_level": 5
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 347,
"aa_ref": "C",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1513,
"cdna_start": 1085,
"cds_end": null,
"cds_length": 1044,
"cds_start": 907,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000473651.5",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.907T>C",
"hgvs_p": "p.Cys303Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424984.1",
"strand": true,
"transcript": "ENST00000473651.5",
"transcript_support_level": 5
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 314,
"aa_ref": "C",
"aa_start": 213,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4906,
"cdna_start": 1330,
"cds_end": null,
"cds_length": 945,
"cds_start": 637,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001321238.2",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.637T>C",
"hgvs_p": "p.Cys213Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308167.1",
"strand": true,
"transcript": "NM_001321238.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 292,
"aa_ref": "C",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3701,
"cdna_start": 1812,
"cds_end": null,
"cds_length": 879,
"cds_start": 571,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001321239.1",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "c.571T>C",
"hgvs_p": "p.Cys191Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308168.1",
"strand": true,
"transcript": "NM_001321239.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3902,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000468227.5",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "n.2338T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000468227.5",
"transcript_support_level": 2
},
{
"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": 7784,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 45,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000471702.2",
"gene_hgnc_id": 48351,
"gene_symbol": "NPHP3-ACAD11",
"hgvs_c": "n.*1980+6572A>G",
"hgvs_p": null,
"intron_rank": 26,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000419763.1",
"strand": false,
"transcript": "ENST00000471702.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 7788,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 45,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_037804.1",
"gene_hgnc_id": 48351,
"gene_symbol": "NPHP3-ACAD11",
"hgvs_c": "n.3995+6572A>G",
"hgvs_p": null,
"intron_rank": 26,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_037804.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1969,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007095728.1",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "n.1854-263T>C",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007095728.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 505,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000494112.1",
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"hgvs_c": "n.-40T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000494112.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1553770577",
"effect": "missense_variant",
"frequency_reference_population": 0.0000027369929,
"gene_hgnc_id": 23230,
"gene_symbol": "UBA5",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000273699,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": "Developmental and epileptic encephalopathy, 44",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.612,
"pos": 132675342,
"ref": "T",
"revel_prediction": "Pathogenic",
"revel_score": 0.728,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.09000000357627869,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.09,
"transcript": "NM_024818.6"
}
]
}