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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: 20-63306041-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=63306041&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1_Moderate",
"PM2"
],
"effects": [
"splice_donor_variant",
"intron_variant"
],
"gene_symbol": "COL20A1",
"hgnc_id": 14670,
"hgvs_c": "c.496+2T>A",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_020882.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2",
"acmg_score": 4,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"chr": "20",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6700000166893005,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1284,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8045,
"cdna_start": null,
"cds_end": null,
"cds_length": 3855,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 36,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_020882.4",
"gene_hgnc_id": 14670,
"gene_symbol": "COL20A1",
"hgvs_c": "c.496+2T>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000358894.11",
"protein_coding": true,
"protein_id": "NP_065933.2",
"strand": true,
"transcript": "NM_020882.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1284,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8045,
"cdna_start": null,
"cds_end": null,
"cds_length": 3855,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 36,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000358894.11",
"gene_hgnc_id": 14670,
"gene_symbol": "COL20A1",
"hgvs_c": "c.496+2T>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020882.4",
"protein_coding": true,
"protein_id": "ENSP00000351767.6",
"strand": true,
"transcript": "ENST00000358894.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4536,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 36,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000479501.5",
"gene_hgnc_id": 14670,
"gene_symbol": "COL20A1",
"hgvs_c": "n.558+2T>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000479501.5",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1297,
"aa_ref": "G",
"aa_start": 166,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8097,
"cdna_start": 566,
"cds_end": null,
"cds_length": 3894,
"cds_start": 498,
"consequences": [
"synonymous_variant"
],
"exon_count": 35,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000422202.5",
"gene_hgnc_id": 14670,
"gene_symbol": "COL20A1",
"hgvs_c": "c.498T>A",
"hgvs_p": "p.Gly166Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000414753.1",
"strand": true,
"transcript": "ENST00000422202.5",
"transcript_support_level": 5
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1280,
"aa_ref": "G",
"aa_start": 166,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4148,
"cdna_start": 586,
"cds_end": null,
"cds_length": 3843,
"cds_start": 498,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000938907.1",
"gene_hgnc_id": 14670,
"gene_symbol": "COL20A1",
"hgvs_c": "c.498T>A",
"hgvs_p": "p.Gly166Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608966.1",
"strand": true,
"transcript": "ENST00000938907.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1336,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4324,
"cdna_start": null,
"cds_end": null,
"cds_length": 4011,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 37,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000894509.1",
"gene_hgnc_id": 14670,
"gene_symbol": "COL20A1",
"hgvs_c": "c.496+2T>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000564568.1",
"strand": true,
"transcript": "ENST00000894509.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1429,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8098,
"cdna_start": null,
"cds_end": null,
"cds_length": 4290,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 36,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011528937.2",
"gene_hgnc_id": 14670,
"gene_symbol": "COL20A1",
"hgvs_c": "c.496+2T>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011527239.1",
"strand": true,
"transcript": "XM_011528937.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1359,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4286,
"cdna_start": null,
"cds_end": null,
"cds_length": 4080,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 36,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011528938.2",
"gene_hgnc_id": 14670,
"gene_symbol": "COL20A1",
"hgvs_c": "c.496+2T>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011527240.1",
"strand": true,
"transcript": "XM_011528938.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999922703309806,
"dbsnp": null,
"effect": "splice_donor_variant,intron_variant",
"frequency_reference_population": 6.9179544e-7,
"gene_hgnc_id": 14670,
"gene_symbol": "COL20A1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.91795e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.374,
"pos": 63306041,
"ref": "T",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.8100000023841858,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.5,
"transcript": "NM_020882.4"
}
]
}