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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: 12-57827556-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57827556&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"gene_symbol": "CTDSP2",
"hgnc_id": 17077,
"hgvs_c": "c.-209A>G",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "ENST00000547701.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 162,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0801,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.25,
"chr": "12",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.17948418855667114,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 119,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 988,
"cdna_start": null,
"cds_end": null,
"cds_length": 360,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000547701.5",
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"hgvs_c": "c.-209A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000446705.1",
"strand": false,
"transcript": "ENST00000547701.5",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 271,
"aa_ref": "Y",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4785,
"cdna_start": 542,
"cds_end": null,
"cds_length": 816,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_005730.4",
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"hgvs_c": "c.248A>G",
"hgvs_p": "p.Tyr83Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000398073.7",
"protein_coding": true,
"protein_id": "NP_005721.3",
"strand": false,
"transcript": "NM_005730.4",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 271,
"aa_ref": "Y",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4785,
"cdna_start": 542,
"cds_end": null,
"cds_length": 816,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000398073.7",
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"hgvs_c": "c.248A>G",
"hgvs_p": "p.Tyr83Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005730.4",
"protein_coding": true,
"protein_id": "ENSP00000381148.2",
"strand": false,
"transcript": "ENST00000398073.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 119,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 988,
"cdna_start": null,
"cds_end": null,
"cds_length": 360,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000547701.5",
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"hgvs_c": "c.-209A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000446705.1",
"strand": false,
"transcript": "ENST00000547701.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 98,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1368,
"cdna_start": null,
"cds_end": null,
"cds_length": 297,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000548823.1",
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"hgvs_c": "c.117+1988A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000447046.1",
"strand": false,
"transcript": "ENST00000548823.1",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 180,
"aa_ref": "Y",
"aa_start": 46,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 544,
"cdna_start": 138,
"cds_end": null,
"cds_length": 543,
"cds_start": 137,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000550144.1",
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"hgvs_c": "c.137A>G",
"hgvs_p": "p.Tyr46Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000448299.1",
"strand": false,
"transcript": "ENST00000550144.1",
"transcript_support_level": 4
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 277,
"aa_ref": "Y",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4803,
"cdna_start": 542,
"cds_end": null,
"cds_length": 834,
"cds_start": 248,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_005268556.3",
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"hgvs_c": "c.248A>G",
"hgvs_p": "p.Tyr83Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005268613.1",
"strand": false,
"transcript": "XM_005268556.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 900,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000551594.1",
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"hgvs_c": "n.248A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000448951.1",
"strand": false,
"transcript": "ENST00000551594.1",
"transcript_support_level": 3
},
{
"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": 436,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000552294.1",
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"hgvs_c": "n.-149A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000552294.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs200585191",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"frequency_reference_population": 0.00010037249,
"gene_hgnc_id": 17077,
"gene_symbol": "CTDSP2",
"gnomad_exomes_ac": 147,
"gnomad_exomes_af": 0.000100561,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 15,
"gnomad_genomes_af": 0.0000985662,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.56,
"pos": 57827556,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.162,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05000000074505806,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.05,
"transcript": "ENST00000547701.5"
}
]
}