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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: 1-179557122-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=179557122&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 179557122,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000367615.9",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.643C>G",
"hgvs_p": "p.Gln215Glu",
"transcript": "NM_014625.4",
"protein_id": "NP_055440.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 383,
"cds_start": 643,
"cds_end": null,
"cds_length": 1152,
"cdna_start": 727,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": "ENST00000367615.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.643C>G",
"hgvs_p": "p.Gln215Glu",
"transcript": "ENST00000367615.9",
"protein_id": "ENSP00000356587.4",
"transcript_support_level": 1,
"aa_start": 215,
"aa_end": null,
"aa_length": 383,
"cds_start": 643,
"cds_end": null,
"cds_length": 1152,
"cdna_start": 727,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": "NM_014625.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.534+2557C>G",
"hgvs_p": null,
"transcript": "ENST00000367616.4",
"protein_id": "ENSP00000356588.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 315,
"cds_start": -4,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.466C>G",
"hgvs_p": "p.Gln156Glu",
"transcript": "XM_005245483.4",
"protein_id": "XP_005245540.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 324,
"cds_start": 466,
"cds_end": null,
"cds_length": 975,
"cdna_start": 550,
"cdna_end": null,
"cdna_length": 1693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.534+2557C>G",
"hgvs_p": null,
"transcript": "NM_001297575.2",
"protein_id": "NP_001284504.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 315,
"cds_start": -4,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.461+2557C>G",
"hgvs_p": null,
"transcript": "XM_017002298.2",
"protein_id": "XP_016857787.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 272,
"cds_start": -4,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1537,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.534+2557C>G",
"hgvs_p": null,
"transcript": "XM_017002299.2",
"protein_id": "XP_016857788.1",
"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": 697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"dbsnp": "rs778055996",
"frequency_reference_population": 0.000034697267,
"hom_count_reference_population": 0,
"allele_count_reference_population": 56,
"gnomad_exomes_af": 0.0000362578,
"gnomad_genomes_af": 0.0000197101,
"gnomad_exomes_ac": 53,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6676985025405884,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.553,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0891,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.812,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.05,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP2",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000367615.9",
"gene_symbol": "NPHS2",
"hgnc_id": 13394,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.643C>G",
"hgvs_p": "p.Gln215Glu"
}
],
"clinvar_disease": " type 2,Nephrotic syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Nephrotic syndrome, type 2",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}