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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: 15-66716485-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=66716485&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 66716485,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000288840.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "c.939G>A",
"hgvs_p": "p.Pro313Pro",
"transcript": "NM_005585.5",
"protein_id": "NP_005576.3",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 496,
"cds_start": 939,
"cds_end": null,
"cds_length": 1491,
"cdna_start": 1962,
"cdna_end": null,
"cdna_length": 3828,
"mane_select": "ENST00000288840.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "c.939G>A",
"hgvs_p": "p.Pro313Pro",
"transcript": "ENST00000288840.10",
"protein_id": "ENSP00000288840.5",
"transcript_support_level": 1,
"aa_start": 313,
"aa_end": null,
"aa_length": 496,
"cds_start": 939,
"cds_end": null,
"cds_length": 1491,
"cdna_start": 1962,
"cdna_end": null,
"cdna_length": 3828,
"mane_select": "NM_005585.5",
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "n.939G>A",
"hgvs_p": null,
"transcript": "ENST00000557916.5",
"protein_id": "ENSP00000452955.1",
"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": 1401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "c.93G>A",
"hgvs_p": "p.Pro31Pro",
"transcript": "ENST00000558937.1",
"protein_id": "ENSP00000452694.1",
"transcript_support_level": 5,
"aa_start": 31,
"aa_end": null,
"aa_length": 55,
"cds_start": 93,
"cds_end": null,
"cds_length": 168,
"cdna_start": 93,
"cdna_end": null,
"cdna_length": 632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "c.156G>A",
"hgvs_p": "p.Pro52Pro",
"transcript": "XM_011521561.3",
"protein_id": "XP_011519863.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 235,
"cds_start": 156,
"cds_end": null,
"cds_length": 708,
"cdna_start": 4769,
"cdna_end": null,
"cdna_length": 6635,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "n.114G>A",
"hgvs_p": null,
"transcript": "ENST00000559931.5",
"protein_id": "ENSP00000453446.1",
"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": 573,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "n.1962G>A",
"hgvs_p": null,
"transcript": "NR_027654.2",
"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": 3960,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "n.*29G>A",
"hgvs_p": null,
"transcript": "XR_931827.3",
"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": 2012,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"dbsnp": "rs144403747",
"frequency_reference_population": 0.000032868054,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000280786,
"gnomad_genomes_af": 0.0000787805,
"gnomad_exomes_ac": 41,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4699999988079071,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.8199999928474426,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.052,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.82,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000288840.10",
"gene_symbol": "SMAD6",
"hgnc_id": 6772,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.939G>A",
"hgvs_p": "p.Pro313Pro"
}
],
"clinvar_disease": "Aortic valve disease 2",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Aortic valve disease 2",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}