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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: 16-90060606-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=90060606&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 90060606,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001098173.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM7",
"gene_hgnc_id": 9351,
"hgvs_c": "c.968G>A",
"hgvs_p": "p.Arg323Gln",
"transcript": "NM_001098173.2",
"protein_id": "NP_001091643.1",
"transcript_support_level": null,
"aa_start": 323,
"aa_end": null,
"aa_length": 492,
"cds_start": 968,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000449207.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001098173.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM7",
"gene_hgnc_id": 9351,
"hgvs_c": "c.968G>A",
"hgvs_p": "p.Arg323Gln",
"transcript": "ENST00000449207.8",
"protein_id": "ENSP00000396732.2",
"transcript_support_level": 1,
"aa_start": 323,
"aa_end": null,
"aa_length": 492,
"cds_start": 968,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001098173.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000449207.8"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRDM7",
"gene_hgnc_id": 9351,
"hgvs_c": "n.473+846G>A",
"hgvs_p": null,
"transcript": "ENST00000325921.10",
"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": "ENST00000325921.10"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM7",
"gene_hgnc_id": 9351,
"hgvs_c": "c.749G>A",
"hgvs_p": "p.Arg250Gln",
"transcript": "XM_017022882.2",
"protein_id": "XP_016878371.1",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 419,
"cds_start": 749,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017022882.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM7",
"gene_hgnc_id": 9351,
"hgvs_c": "c.749G>A",
"hgvs_p": "p.Arg250Gln",
"transcript": "XM_017022883.2",
"protein_id": "XP_016878372.1",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 419,
"cds_start": 749,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017022883.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM7",
"gene_hgnc_id": 9351,
"hgvs_c": "c.431G>A",
"hgvs_p": "p.Arg144Gln",
"transcript": "XM_017022884.2",
"protein_id": "XP_016878373.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 313,
"cds_start": 431,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017022884.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PRDM7",
"gene_hgnc_id": 9351,
"hgvs_c": "c.950+846G>A",
"hgvs_p": null,
"transcript": "XM_011522829.2",
"protein_id": "XP_011521131.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 377,
"cds_start": null,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011522829.2"
}
],
"gene_symbol": "PRDM7",
"gene_hgnc_id": 9351,
"dbsnp": "rs201215666",
"frequency_reference_population": 0.000047704958,
"hom_count_reference_population": 0,
"allele_count_reference_population": 77,
"gnomad_exomes_af": 0.0000417286,
"gnomad_genomes_af": 0.000105083,
"gnomad_exomes_ac": 61,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06331056356430054,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.127,
"revel_prediction": "Benign",
"alphamissense_score": 0.1336,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.624,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001098173.2",
"gene_symbol": "PRDM7",
"hgnc_id": 9351,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.968G>A",
"hgvs_p": "p.Arg323Gln"
}
],
"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
}