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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: 17-4960245-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4960245&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 4960245,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004890.3",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.316A>G",
"hgvs_p": "p.Ile106Val",
"transcript": "NM_004890.3",
"protein_id": "NP_004881.2",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 227,
"cds_start": 316,
"cds_end": null,
"cds_length": 684,
"cdna_start": 329,
"cdna_end": null,
"cdna_length": 1005,
"mane_select": "ENST00000206020.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.316A>G",
"hgvs_p": "p.Ile106Val",
"transcript": "ENST00000206020.8",
"protein_id": "ENSP00000206020.3",
"transcript_support_level": 1,
"aa_start": 106,
"aa_end": null,
"aa_length": 227,
"cds_start": 316,
"cds_end": null,
"cds_length": 684,
"cdna_start": 329,
"cdna_end": null,
"cdna_length": 1005,
"mane_select": "NM_004890.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.283A>G",
"hgvs_p": "p.Ile95Val",
"transcript": "ENST00000575142.5",
"protein_id": "ENSP00000461145.1",
"transcript_support_level": 1,
"aa_start": 95,
"aa_end": null,
"aa_length": 194,
"cds_start": 283,
"cds_end": null,
"cds_length": 585,
"cdna_start": 302,
"cdna_end": null,
"cdna_length": 1094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "c.163A>G",
"hgvs_p": "p.Ile55Val",
"transcript": "ENST00000573366.5",
"protein_id": "ENSP00000458405.1",
"transcript_support_level": 3,
"aa_start": 55,
"aa_end": null,
"aa_length": 176,
"cds_start": 163,
"cds_end": null,
"cds_length": 531,
"cdna_start": 1022,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "n.237A>G",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "n.437A>G",
"hgvs_p": null,
"transcript": "ENST00000573805.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"hgvs_c": "n.210-55A>G",
"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
}
],
"gene_symbol": "SPAG7",
"gene_hgnc_id": 11216,
"dbsnp": "rs73343382",
"frequency_reference_population": 0.0059279893,
"hom_count_reference_population": 465,
"allele_count_reference_population": 9568,
"gnomad_exomes_af": 0.00333077,
"gnomad_genomes_af": 0.0308706,
"gnomad_exomes_ac": 4869,
"gnomad_genomes_ac": 4699,
"gnomad_exomes_homalt": 233,
"gnomad_genomes_homalt": 232,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0028620362281799316,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.078,
"revel_prediction": "Benign",
"alphamissense_score": 0.111,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.796,
"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": "NM_004890.3",
"gene_symbol": "SPAG7",
"hgnc_id": 11216,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.316A>G",
"hgvs_p": "p.Ile106Val"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}