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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: 19-35845512-TCCGGGGTGGGGCGGCCACGCCCTCCAGCCTGTGGAA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=35845512&ref=TCCGGGGTGGGGCGGCCACGCCCTCCAGCCTGTGGAA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 35845512,
"ref": "TCCGGGGTGGGGCGGCCACGCCCTCCAGCCTGTGGAA",
"alt": "T",
"effect": "frameshift_variant,splice_acceptor_variant,splice_region_variant,intron_variant",
"transcript": "NM_004646.4",
"consequences": [
{
"aa_ref": "RLEGVAAPPR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS1",
"gene_hgnc_id": 7908,
"hgvs_c": "c.1758-8_1785delTTCCACAGGCTGGAGGGCGTGGCCGCCCCACCCCGG",
"hgvs_p": "p.Leu587fs",
"transcript": "NM_004646.4",
"protein_id": "NP_004637.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
"aa_length": 1241,
"cds_start": 1758,
"cds_end": null,
"cds_length": 3726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000378910.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004646.4"
},
{
"aa_ref": "RLEGVAAPPR",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS1",
"gene_hgnc_id": 7908,
"hgvs_c": "c.1758-8_1785delTTCCACAGGCTGGAGGGCGTGGCCGCCCCACCCCGG",
"hgvs_p": "p.Leu587fs",
"transcript": "ENST00000378910.10",
"protein_id": "ENSP00000368190.4",
"transcript_support_level": 1,
"aa_start": 586,
"aa_end": null,
"aa_length": 1241,
"cds_start": 1758,
"cds_end": null,
"cds_length": 3726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004646.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378910.10"
},
{
"aa_ref": "RLEGVAAPPR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS1",
"gene_hgnc_id": 7908,
"hgvs_c": "c.1698-8_1725delTTCCACAGGCTGGAGGGCGTGGCCGCCCCACCCCGG",
"hgvs_p": "p.Leu567fs",
"transcript": "ENST00000869106.1",
"protein_id": "ENSP00000539165.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 1221,
"cds_start": 1698,
"cds_end": null,
"cds_length": 3666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869106.1"
},
{
"aa_ref": "RLEGVAAPPR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS1",
"gene_hgnc_id": 7908,
"hgvs_c": "c.1758-8_1785delTTCCACAGGCTGGAGGGCGTGGCCGCCCCACCCCGG",
"hgvs_p": "p.Leu587fs",
"transcript": "ENST00000353632.6",
"protein_id": "ENSP00000343634.5",
"transcript_support_level": 5,
"aa_start": 586,
"aa_end": null,
"aa_length": 1201,
"cds_start": 1758,
"cds_end": null,
"cds_length": 3606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000353632.6"
},
{
"aa_ref": "RLEGVAAPPR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS1",
"gene_hgnc_id": 7908,
"hgvs_c": "c.1563-8_1590delTTCCACAGGCTGGAGGGCGTGGCCGCCCCACCCCGG",
"hgvs_p": "p.Leu522fs",
"transcript": "ENST00000869107.1",
"protein_id": "ENSP00000539166.1",
"transcript_support_level": null,
"aa_start": 521,
"aa_end": null,
"aa_length": 1176,
"cds_start": 1563,
"cds_end": null,
"cds_length": 3531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869107.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHS1",
"gene_hgnc_id": 7908,
"hgvs_c": "n.-38_-3delTTCCACAGGCTGGAGGGCGTGGCCGCCCCACCCCGG",
"hgvs_p": null,
"transcript": "ENST00000585400.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000585400.1"
}
],
"gene_symbol": "NPHS1",
"gene_hgnc_id": 7908,
"dbsnp": "rs386833891",
"frequency_reference_population": 0.0000027429273,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000274293,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.097,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_004646.4",
"gene_symbol": "NPHS1",
"hgnc_id": 7908,
"effects": [
"frameshift_variant",
"splice_acceptor_variant",
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1758-8_1785delTTCCACAGGCTGGAGGGCGTGGCCGCCCCACCCCGG",
"hgvs_p": "p.Leu587fs"
}
],
"clinvar_disease": "Finnish congenital nephrotic syndrome,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Finnish congenital nephrotic syndrome|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}