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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: 8-47774239-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=47774239&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 47774239,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_006904.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 86,
"exon_rank_end": null,
"exon_count": 86,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.12321G>A",
"hgvs_p": "p.Leu4107Leu",
"transcript": "NM_006904.7",
"protein_id": "NP_008835.5",
"transcript_support_level": null,
"aa_start": 4107,
"aa_end": null,
"aa_length": 4128,
"cds_start": 12321,
"cds_end": null,
"cds_length": 12387,
"cdna_start": 12331,
"cdna_end": null,
"cdna_length": 13459,
"mane_select": "ENST00000314191.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 86,
"exon_rank_end": null,
"exon_count": 86,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.12321G>A",
"hgvs_p": "p.Leu4107Leu",
"transcript": "ENST00000314191.7",
"protein_id": "ENSP00000313420.3",
"transcript_support_level": 1,
"aa_start": 4107,
"aa_end": null,
"aa_length": 4128,
"cds_start": 12321,
"cds_end": null,
"cds_length": 12387,
"cdna_start": 12331,
"cdna_end": null,
"cdna_length": 13459,
"mane_select": "NM_006904.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 85,
"exon_rank_end": null,
"exon_count": 85,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.12228G>A",
"hgvs_p": "p.Leu4076Leu",
"transcript": "ENST00000338368.7",
"protein_id": "ENSP00000345182.4",
"transcript_support_level": 1,
"aa_start": 4076,
"aa_end": null,
"aa_length": 4097,
"cds_start": 12228,
"cds_end": null,
"cds_length": 12294,
"cdna_start": 12280,
"cdna_end": null,
"cdna_length": 12784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 85,
"exon_rank_end": null,
"exon_count": 85,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.12228G>A",
"hgvs_p": "p.Leu4076Leu",
"transcript": "NM_001081640.2",
"protein_id": "NP_001075109.1",
"transcript_support_level": null,
"aa_start": 4076,
"aa_end": null,
"aa_length": 4097,
"cds_start": 12228,
"cds_end": null,
"cds_length": 12294,
"cdna_start": 12238,
"cdna_end": null,
"cdna_length": 13366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.4998G>A",
"hgvs_p": "p.Leu1666Leu",
"transcript": "ENST00000697603.1",
"protein_id": "ENSP00000513358.1",
"transcript_support_level": null,
"aa_start": 1666,
"aa_end": null,
"aa_length": 1687,
"cds_start": 4998,
"cds_end": null,
"cds_length": 5064,
"cdna_start": 5179,
"cdna_end": null,
"cdna_length": 6282,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.729G>A",
"hgvs_p": null,
"transcript": "ENST00000536483.1",
"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": 834,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.1592G>A",
"hgvs_p": null,
"transcript": "ENST00000697601.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2695,
"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": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.2894G>A",
"hgvs_p": null,
"transcript": "ENST00000697602.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3997,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.2331G>A",
"hgvs_p": null,
"transcript": "ENST00000697604.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.*136G>A",
"hgvs_p": null,
"transcript": "ENST00000536429.1",
"protein_id": "ENSP00000442177.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 89,
"cds_start": -4,
"cds_end": null,
"cds_length": 270,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"dbsnp": "rs192400758",
"frequency_reference_population": 0.000046762187,
"hom_count_reference_population": 0,
"allele_count_reference_population": 75,
"gnomad_exomes_af": 0.0000461583,
"gnomad_genomes_af": 0.0000525169,
"gnomad_exomes_ac": 67,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3700000047683716,
"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": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.92,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_006904.7",
"gene_symbol": "PRKDC",
"hgnc_id": 9413,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.12321G>A",
"hgvs_p": "p.Leu4107Leu"
}
],
"clinvar_disease": "Severe combined immunodeficiency due to DNA-PKcs deficiency,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"phenotype_combined": "not provided|Severe combined immunodeficiency due to DNA-PKcs deficiency",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}