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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: 3-42690871-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=42690871&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 15,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "KLHL40",
"hgnc_id": 30372,
"hgvs_c": "c.1620C>T",
"hgvs_p": "p.Phe540Phe",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -15,
"transcript": "NM_152393.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7,BS1,BS2",
"acmg_score": -15,
"allele_count_reference_population": 677,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.68,
"chr": "3",
"clinvar_classification": "Benign",
"clinvar_disease": "Nemaline myopathy 8",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6800000071525574,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 621,
"aa_ref": "F",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2499,
"cdna_start": 1702,
"cds_end": null,
"cds_length": 1866,
"cds_start": 1620,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_152393.4",
"gene_hgnc_id": 30372,
"gene_symbol": "KLHL40",
"hgvs_c": "c.1620C>T",
"hgvs_p": "p.Phe540Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000287777.5",
"protein_coding": true,
"protein_id": "NP_689606.2",
"strand": true,
"transcript": "NM_152393.4",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 621,
"aa_ref": "F",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2499,
"cdna_start": 1702,
"cds_end": null,
"cds_length": 1866,
"cds_start": 1620,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000287777.5",
"gene_hgnc_id": 30372,
"gene_symbol": "KLHL40",
"hgvs_c": "c.1620C>T",
"hgvs_p": "p.Phe540Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_152393.4",
"protein_coding": true,
"protein_id": "ENSP00000287777.4",
"strand": true,
"transcript": "ENST00000287777.5",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 616,
"aa_ref": "F",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2380,
"cdna_start": 1687,
"cds_end": null,
"cds_length": 1851,
"cds_start": 1605,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000942348.1",
"gene_hgnc_id": 30372,
"gene_symbol": "KLHL40",
"hgvs_c": "c.1605C>T",
"hgvs_p": "p.Phe535Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612407.1",
"strand": true,
"transcript": "ENST00000942348.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 614,
"aa_ref": "F",
"aa_start": 533,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2356,
"cdna_start": 1676,
"cds_end": null,
"cds_length": 1845,
"cds_start": 1599,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000942349.1",
"gene_hgnc_id": 30372,
"gene_symbol": "KLHL40",
"hgvs_c": "c.1599C>T",
"hgvs_p": "p.Phe533Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612408.1",
"strand": true,
"transcript": "ENST00000942349.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 585,
"aa_ref": "F",
"aa_start": 504,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5001,
"cdna_start": 1684,
"cds_end": null,
"cds_length": 1758,
"cds_start": 1512,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000942345.1",
"gene_hgnc_id": 30372,
"gene_symbol": "KLHL40",
"hgvs_c": "c.1512C>T",
"hgvs_p": "p.Phe504Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612404.1",
"strand": true,
"transcript": "ENST00000942345.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 559,
"aa_ref": "F",
"aa_start": 478,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2213,
"cdna_start": 1517,
"cds_end": null,
"cds_length": 1680,
"cds_start": 1434,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000942347.1",
"gene_hgnc_id": 30372,
"gene_symbol": "KLHL40",
"hgvs_c": "c.1434C>T",
"hgvs_p": "p.Phe478Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612406.1",
"strand": true,
"transcript": "ENST00000942347.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 523,
"aa_ref": "F",
"aa_start": 442,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2105,
"cdna_start": 1408,
"cds_end": null,
"cds_length": 1572,
"cds_start": 1326,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000942346.1",
"gene_hgnc_id": 30372,
"gene_symbol": "KLHL40",
"hgvs_c": "c.1326C>T",
"hgvs_p": "p.Phe442Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612405.1",
"strand": true,
"transcript": "ENST00000942346.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199888675",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00042077026,
"gene_hgnc_id": 30372,
"gene_symbol": "KLHL40",
"gnomad_exomes_ac": 629,
"gnomad_exomes_af": 0.0004318,
"gnomad_exomes_homalt": 9,
"gnomad_genomes_ac": 48,
"gnomad_genomes_af": 0.000315246,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 9,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "Nemaline myopathy 8",
"phylop100way_prediction": "Benign",
"phylop100way_score": -2.802,
"pos": 42690871,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07000000029802322,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.07,
"transcript": "NM_152393.4"
}
]
}