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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: 1-3430888-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=3430888&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 3430888,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000270722.10",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.3301G>A",
"hgvs_p": "p.Val1101Met",
"transcript": "NM_022114.4",
"protein_id": "NP_071397.3",
"transcript_support_level": null,
"aa_start": 1101,
"aa_end": null,
"aa_length": 1276,
"cds_start": 3301,
"cds_end": null,
"cds_length": 3831,
"cdna_start": 3358,
"cdna_end": null,
"cdna_length": 8698,
"mane_select": "ENST00000270722.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.3301G>A",
"hgvs_p": "p.Val1101Met",
"transcript": "ENST00000270722.10",
"protein_id": "ENSP00000270722.5",
"transcript_support_level": 1,
"aa_start": 1101,
"aa_end": null,
"aa_length": 1276,
"cds_start": 3301,
"cds_end": null,
"cds_length": 3831,
"cdna_start": 3358,
"cdna_end": null,
"cdna_length": 8698,
"mane_select": "NM_022114.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.3301G>A",
"hgvs_p": "p.Val1101Met",
"transcript": "ENST00000378391.6",
"protein_id": "ENSP00000367643.2",
"transcript_support_level": 1,
"aa_start": 1101,
"aa_end": null,
"aa_length": 1257,
"cds_start": 3301,
"cds_end": null,
"cds_length": 3774,
"cdna_start": 3364,
"cdna_end": null,
"cdna_length": 5447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "n.3079G>A",
"hgvs_p": null,
"transcript": "ENST00000512462.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.3301G>A",
"hgvs_p": "p.Val1101Met",
"transcript": "NM_199454.3",
"protein_id": "NP_955533.2",
"transcript_support_level": null,
"aa_start": 1101,
"aa_end": null,
"aa_length": 1257,
"cds_start": 3301,
"cds_end": null,
"cds_length": 3774,
"cdna_start": 3358,
"cdna_end": null,
"cdna_length": 8641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.3304G>A",
"hgvs_p": "p.Val1102Met",
"transcript": "ENST00000511072.5",
"protein_id": "ENSP00000426975.1",
"transcript_support_level": 5,
"aa_start": 1102,
"aa_end": null,
"aa_length": 1178,
"cds_start": 3304,
"cds_end": null,
"cds_length": 3537,
"cdna_start": 3396,
"cdna_end": null,
"cdna_length": 4282,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.3301G>A",
"hgvs_p": "p.Val1101Met",
"transcript": "ENST00000514189.5",
"protein_id": "ENSP00000421400.1",
"transcript_support_level": 5,
"aa_start": 1101,
"aa_end": null,
"aa_length": 1177,
"cds_start": 3301,
"cds_end": null,
"cds_length": 3534,
"cdna_start": 3350,
"cdna_end": null,
"cdna_length": 4236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.2725G>A",
"hgvs_p": "p.Val909Met",
"transcript": "ENST00000509860.1",
"protein_id": "ENSP00000425796.1",
"transcript_support_level": 5,
"aa_start": 909,
"aa_end": null,
"aa_length": 1084,
"cds_start": 2725,
"cds_end": null,
"cds_length": 3255,
"cdna_start": 2725,
"cdna_end": null,
"cdna_length": 3737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "n.503G>A",
"hgvs_p": null,
"transcript": "ENST00000378389.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 1142,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"dbsnp": "rs201654872",
"frequency_reference_population": 0.0014924597,
"hom_count_reference_population": 46,
"allele_count_reference_population": 2409,
"gnomad_exomes_af": 0.00156522,
"gnomad_genomes_af": 0.000794266,
"gnomad_exomes_ac": 2288,
"gnomad_genomes_ac": 121,
"gnomad_exomes_homalt": 43,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005124121904373169,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.033,
"revel_prediction": "Benign",
"alphamissense_score": 0.0817,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.224,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000270722.10",
"gene_symbol": "PRDM16",
"hgnc_id": 14000,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3301G>A",
"hgvs_p": "p.Val1101Met"
}
],
"clinvar_disease": " 1LL, dilated,Cardiomyopathy,Left ventricular noncompaction 8,PRDM16-related disorder,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "Cardiomyopathy, dilated, 1LL|Left ventricular noncompaction 8|not specified|PRDM16-related disorder|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}