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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: 1-179575915-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=179575915&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 179575915,
"ref": "C",
"alt": "A",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"transcript": "ENST00000367615.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"hgvs_p": null,
"transcript": "NM_014625.4",
"protein_id": "NP_055440.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 383,
"cds_start": -4,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": "ENST00000367615.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"hgvs_p": null,
"transcript": "ENST00000367615.9",
"protein_id": "ENSP00000356587.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 383,
"cds_start": -4,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"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": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"hgvs_p": null,
"transcript": "NM_014625.4",
"protein_id": "NP_055440.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 383,
"cds_start": -4,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": "ENST00000367615.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"hgvs_p": null,
"transcript": "ENST00000367615.9",
"protein_id": "ENSP00000356587.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 383,
"cds_start": -4,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"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": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"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": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"hgvs_p": null,
"transcript": "XM_005245483.4",
"protein_id": "XP_005245540.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": -4,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"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": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"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": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"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": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"hgvs_p": null,
"transcript": "XM_005245483.4",
"protein_id": "XP_005245540.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": -4,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"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": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"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": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS2",
"gene_hgnc_id": 13394,
"hgvs_c": "c.-51G>T",
"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": "rs12406197",
"frequency_reference_population": 0.25969738,
"hom_count_reference_population": 47137,
"allele_count_reference_population": 352788,
"gnomad_exomes_af": 0.262603,
"gnomad_genomes_af": 0.236664,
"gnomad_exomes_ac": 316772,
"gnomad_genomes_ac": 36016,
"gnomad_exomes_homalt": 42631,
"gnomad_genomes_homalt": 4506,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7099999785423279,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.143,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000367615.9",
"gene_symbol": "NPHS2",
"hgnc_id": 13394,
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.-51G>T",
"hgvs_p": null
}
],
"clinvar_disease": " type 2,Focal segmental glomerulosclerosis,NPHS2-related disorder,Nephrotic syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:1 B:9",
"phenotype_combined": "Nephrotic syndrome, type 2|not specified|not provided|Focal segmental glomerulosclerosis|NPHS2-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}