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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: 3-132681095-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=132681095&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 132681095,
"ref": "C",
"alt": "T",
"effect": "3_prime_UTR_variant",
"transcript": "NM_153240.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.*815G>A",
"hgvs_p": null,
"transcript": "NM_153240.5",
"protein_id": "NP_694972.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1330,
"cds_start": null,
"cds_end": null,
"cds_length": 3993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000337331.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153240.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.*815G>A",
"hgvs_p": null,
"transcript": "ENST00000337331.10",
"protein_id": "ENSP00000338766.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1330,
"cds_start": null,
"cds_end": null,
"cds_length": 3993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_153240.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000337331.10"
},
{
"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+819G>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": null,
"cds_end": null,
"cds_length": 694,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000632629.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.*815G>A",
"hgvs_p": null,
"transcript": "ENST00000971412.1",
"protein_id": "ENSP00000641471.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1189,
"cds_start": null,
"cds_end": null,
"cds_length": 3570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971412.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.4007G>A",
"hgvs_p": null,
"transcript": "ENST00000474871.5",
"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": "ENST00000474871.5"
},
{
"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": 45,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.*1980+819G>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": 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": "ENST00000471702.2"
},
{
"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+819G>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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_037804.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.*815G>A",
"hgvs_p": null,
"transcript": "ENST00000971413.1",
"protein_id": "ENSP00000641472.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1263,
"cds_start": null,
"cds_end": null,
"cds_length": 3792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971413.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.*187G>A",
"hgvs_p": null,
"transcript": "ENST00000493732.5",
"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": "ENST00000493732.5"
}
],
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"dbsnp": "rs141464909",
"frequency_reference_population": 0.0057925708,
"hom_count_reference_population": 11,
"allele_count_reference_population": 882,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": 0.00579257,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": 882,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 11,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"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": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.305,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_153240.5",
"gene_symbol": "NPHP3",
"hgnc_id": 7907,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*815G>A",
"hgvs_p": null
},
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000632629.1",
"gene_symbol": "NPHP3-ACAD11",
"hgnc_id": 48351,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.635+819G>A",
"hgvs_p": null
}
],
"clinvar_disease": "NPHP3-related Meckel-like syndrome,Nephronophthisis 3,Renal-hepatic-pancreatic dysplasia 1,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:2",
"phenotype_combined": "NPHP3-related Meckel-like syndrome|Renal-hepatic-pancreatic dysplasia 1|Nephronophthisis 3|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}