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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: 1-3412369-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=3412369&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 3412369,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000270722.10",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.2172G>A",
"hgvs_p": "p.Ala724Ala",
"transcript": "NM_022114.4",
"protein_id": "NP_071397.3",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1276,
"cds_start": 2172,
"cds_end": null,
"cds_length": 3831,
"cdna_start": 2229,
"cdna_end": null,
"cdna_length": 8698,
"mane_select": "ENST00000270722.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.2172G>A",
"hgvs_p": "p.Ala724Ala",
"transcript": "ENST00000270722.10",
"protein_id": "ENSP00000270722.5",
"transcript_support_level": 1,
"aa_start": 724,
"aa_end": null,
"aa_length": 1276,
"cds_start": 2172,
"cds_end": null,
"cds_length": 3831,
"cdna_start": 2229,
"cdna_end": null,
"cdna_length": 8698,
"mane_select": "NM_022114.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.2172G>A",
"hgvs_p": "p.Ala724Ala",
"transcript": "ENST00000378391.6",
"protein_id": "ENSP00000367643.2",
"transcript_support_level": 1,
"aa_start": 724,
"aa_end": null,
"aa_length": 1257,
"cds_start": 2172,
"cds_end": null,
"cds_length": 3774,
"cdna_start": 2235,
"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": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "n.1950G>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": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.2172G>A",
"hgvs_p": "p.Ala724Ala",
"transcript": "NM_199454.3",
"protein_id": "NP_955533.2",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1257,
"cds_start": 2172,
"cds_end": null,
"cds_length": 3774,
"cdna_start": 2229,
"cdna_end": null,
"cdna_length": 8641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.2175G>A",
"hgvs_p": "p.Ala725Ala",
"transcript": "ENST00000511072.5",
"protein_id": "ENSP00000426975.1",
"transcript_support_level": 5,
"aa_start": 725,
"aa_end": null,
"aa_length": 1178,
"cds_start": 2175,
"cds_end": null,
"cds_length": 3537,
"cdna_start": 2267,
"cdna_end": null,
"cdna_length": 4282,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.2175G>A",
"hgvs_p": "p.Ala725Ala",
"transcript": "ENST00000514189.5",
"protein_id": "ENSP00000421400.1",
"transcript_support_level": 5,
"aa_start": 725,
"aa_end": null,
"aa_length": 1177,
"cds_start": 2175,
"cds_end": null,
"cds_length": 3534,
"cdna_start": 2224,
"cdna_end": null,
"cdna_length": 4236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"hgvs_c": "c.1599G>A",
"hgvs_p": "p.Ala533Ala",
"transcript": "ENST00000509860.1",
"protein_id": "ENSP00000425796.1",
"transcript_support_level": 5,
"aa_start": 533,
"aa_end": null,
"aa_length": 1084,
"cds_start": 1599,
"cds_end": null,
"cds_length": 3255,
"cdna_start": 1599,
"cdna_end": null,
"cdna_length": 3737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRDM16",
"gene_hgnc_id": 14000,
"dbsnp": "rs773130347",
"frequency_reference_population": 0.000051441093,
"hom_count_reference_population": 0,
"allele_count_reference_population": 83,
"gnomad_exomes_af": 0.0000362719,
"gnomad_genomes_af": 0.000196967,
"gnomad_exomes_ac": 53,
"gnomad_genomes_ac": 30,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.44999998807907104,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.911,
"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": -15,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -15,
"benign_score": 15,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000270722.10",
"gene_symbol": "PRDM16",
"hgnc_id": 14000,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2172G>A",
"hgvs_p": "p.Ala724Ala"
}
],
"clinvar_disease": "Left ventricular noncompaction 8,PRDM16-related disorder,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3",
"phenotype_combined": "Left ventricular noncompaction 8|not provided|PRDM16-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}