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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: 3-132719848-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=132719848&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 132719848,
"ref": "G",
"alt": "C",
"effect": "intron_variant",
"transcript": "NM_153240.5",
"consequences": [
{
"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": 27,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.394-18C>G",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.394-18C>G",
"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": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.394-18C>G",
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.394-18C>G",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.100-18C>G",
"hgvs_p": null,
"transcript": "ENST00000465756.5",
"protein_id": "ENSP00000419907.1",
"transcript_support_level": 5,
"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": "ENST00000465756.5"
},
{
"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": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.46-18C>G",
"hgvs_p": null,
"transcript": "ENST00000469232.5",
"protein_id": "ENSP00000418664.1",
"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": "ENST00000469232.5"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.34-18C>G",
"hgvs_p": null,
"transcript": "ENST00000471145.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000471145.1"
},
{
"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": 45,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.394-18C>G",
"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": 25,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.100-18C>G",
"hgvs_p": null,
"transcript": "ENST00000684294.1",
"protein_id": "ENSP00000508078.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000684294.1"
},
{
"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": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.117-18C>G",
"hgvs_p": null,
"transcript": "ENST00000684756.1",
"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": "retained_intron",
"feature": "ENST00000684756.1"
},
{
"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": 45,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.498-18C>G",
"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"
}
],
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"dbsnp": "rs886038737",
"frequency_reference_population": 0.0000038946423,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000143931,
"gnomad_genomes_af": 0.0000264859,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.2800000011920929,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.485,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.28,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP6",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "NM_153240.5",
"gene_symbol": "NPHP3",
"hgnc_id": 7907,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.394-18C>G",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000471702.2",
"gene_symbol": "NPHP3-ACAD11",
"hgnc_id": 48351,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.394-18C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Nephronophthisis,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "not specified|Nephronophthisis",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}