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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: 17-4959852-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4959852&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 4959852,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004890.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.482G>A",
"hgvs_p": "p.Ser161Asn",
"transcript": "NM_004890.3",
"protein_id": "NP_004881.2",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 227,
"cds_start": 482,
"cds_end": null,
"cds_length": 684,
"cdna_start": 495,
"cdna_end": null,
"cdna_length": 1005,
"mane_select": "ENST00000206020.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.482G>A",
"hgvs_p": "p.Ser161Asn",
"transcript": "ENST00000206020.8",
"protein_id": "ENSP00000206020.3",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 227,
"cds_start": 482,
"cds_end": null,
"cds_length": 684,
"cdna_start": 495,
"cdna_end": null,
"cdna_length": 1005,
"mane_select": "NM_004890.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.449G>A",
"hgvs_p": "p.Ser150Asn",
"transcript": "ENST00000575142.5",
"protein_id": "ENSP00000461145.1",
"transcript_support_level": 1,
"aa_start": 150,
"aa_end": null,
"aa_length": 194,
"cds_start": 449,
"cds_end": null,
"cds_length": 585,
"cdna_start": 468,
"cdna_end": null,
"cdna_length": 1094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.329G>A",
"hgvs_p": "p.Ser110Asn",
"transcript": "ENST00000573366.5",
"protein_id": "ENSP00000458405.1",
"transcript_support_level": 3,
"aa_start": 110,
"aa_end": null,
"aa_length": 176,
"cds_start": 329,
"cds_end": null,
"cds_length": 531,
"cdna_start": 1188,
"cdna_end": null,
"cdna_length": 1668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "n.*179G>A",
"hgvs_p": null,
"transcript": "ENST00000575784.2",
"protein_id": "ENSP00000458264.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "n.*179G>A",
"hgvs_p": null,
"transcript": "ENST00000575784.2",
"protein_id": "ENSP00000458264.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "n.*132G>A",
"hgvs_p": null,
"transcript": "ENST00000572148.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 498,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"dbsnp": "rs1273912203",
"frequency_reference_population": 0.0000061571045,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.0000061571,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.16459715366363525,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.089,
"revel_prediction": "Benign",
"alphamissense_score": 0.2317,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.593,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004890.3",
"gene_symbol": "SPAG7",
"hgnc_id": 11216,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.482G>A",
"hgvs_p": "p.Ser161Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}