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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: 11-66052385-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=66052385&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 66052385,
"ref": "A",
"alt": "T",
"effect": "initiator_codon_variant",
"transcript": "NM_006842.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "NM_006842.3",
"protein_id": "NP_006833.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 895,
"cds_start": 1,
"cds_end": null,
"cds_length": 2688,
"cdna_start": 22,
"cdna_end": null,
"cdna_length": 3272,
"mane_select": "ENST00000322535.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000322535.11",
"protein_id": "ENSP00000318861.6",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 895,
"cds_start": 1,
"cds_end": null,
"cds_length": 2688,
"cdna_start": 22,
"cdna_end": null,
"cdna_length": 3272,
"mane_select": "NM_006842.3",
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "n.20A>T",
"hgvs_p": null,
"transcript": "ENST00000531041.1",
"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": 1440,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000528302.5",
"protein_id": "ENSP00000432655.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 878,
"cds_start": 1,
"cds_end": null,
"cds_length": 2637,
"cdna_start": 55,
"cdna_end": null,
"cdna_length": 3254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000533595.5",
"protein_id": "ENSP00000431908.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 352,
"cds_start": 1,
"cds_end": null,
"cds_length": 1061,
"cdna_start": 21,
"cdna_end": null,
"cdna_length": 1081,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000524627.5",
"protein_id": "ENSP00000435495.1",
"transcript_support_level": 3,
"aa_start": 1,
"aa_end": null,
"aa_length": 272,
"cds_start": 1,
"cds_end": null,
"cds_length": 821,
"cdna_start": 21,
"cdna_end": null,
"cdna_length": 841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "XM_005273726.5",
"protein_id": "XP_005273783.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 894,
"cds_start": 1,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 22,
"cdna_end": null,
"cdna_length": 3269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "XM_011544740.4",
"protein_id": "XP_011543042.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 894,
"cds_start": 1,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 22,
"cdna_end": null,
"cdna_length": 3269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"initiator_codon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?",
"transcript": "XM_017017144.3",
"protein_id": "XP_016872633.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 893,
"cds_start": 1,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 22,
"cdna_end": null,
"cdna_length": 3266,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "n.620A>T",
"hgvs_p": null,
"transcript": "ENST00000534307.1",
"protein_id": null,
"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": 625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.-15A>T",
"hgvs_p": null,
"transcript": "ENST00000530322.5",
"protein_id": "ENSP00000431520.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 386,
"cds_start": -4,
"cds_end": null,
"cds_length": 1163,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "c.-401A>T",
"hgvs_p": null,
"transcript": "ENST00000524475.1",
"protein_id": "ENSP00000435765.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 79,
"cds_start": -4,
"cds_end": null,
"cds_length": 242,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 432,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "n.-8A>T",
"hgvs_p": null,
"transcript": "ENST00000531589.5",
"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": 616,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"hgvs_c": "n.*66A>T",
"hgvs_p": null,
"transcript": "ENST00000529577.5",
"protein_id": null,
"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": 606,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SF3B2",
"gene_hgnc_id": 10769,
"dbsnp": "rs2135031513",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9792219400405884,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.285,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.817,
"phylop100way_prediction": "Uncertain_significance",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006842.3",
"gene_symbol": "SF3B2",
"hgnc_id": 10769,
"effects": [
"initiator_codon_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1A>T",
"hgvs_p": "p.Met1?"
}
],
"clinvar_disease": "Craniofacial microsomia 1",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Craniofacial microsomia 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}