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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: 17-42423033-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=42423033&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 42423033,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_012232.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAVIN1",
"gene_hgnc_id": 9688,
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"transcript": "NM_012232.6",
"protein_id": "NP_036364.2",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 390,
"cds_start": 65,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000357037.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012232.6"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAVIN1",
"gene_hgnc_id": 9688,
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"transcript": "ENST00000357037.6",
"protein_id": "ENSP00000349541.4",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 390,
"cds_start": 65,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012232.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357037.6"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAVIN1",
"gene_hgnc_id": 9688,
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"transcript": "ENST00000944723.1",
"protein_id": "ENSP00000614782.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 339,
"cds_start": 65,
"cds_end": null,
"cds_length": 1020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944723.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAVIN1",
"gene_hgnc_id": 9688,
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"transcript": "ENST00000944722.1",
"protein_id": "ENSP00000614781.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 335,
"cds_start": 65,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944722.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAVIN1",
"gene_hgnc_id": 9688,
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"transcript": "ENST00000870236.1",
"protein_id": "ENSP00000540295.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 329,
"cds_start": 65,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870236.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAVIN1",
"gene_hgnc_id": 9688,
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"transcript": "XM_005257242.5",
"protein_id": "XP_005257299.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 225,
"cds_start": 65,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005257242.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294400",
"gene_hgnc_id": null,
"hgvs_c": "n.466G>A",
"hgvs_p": null,
"transcript": "ENST00000723360.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000723360.1"
},
{
"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": "LOC102725238",
"gene_hgnc_id": null,
"hgvs_c": "n.-155G>A",
"hgvs_p": null,
"transcript": "XR_007065758.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007065758.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC102725238",
"gene_hgnc_id": null,
"hgvs_c": "n.-154G>A",
"hgvs_p": null,
"transcript": "XR_934763.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_934763.2"
}
],
"gene_symbol": "CAVIN1",
"gene_hgnc_id": 9688,
"dbsnp": "rs61729285",
"frequency_reference_population": 0.00019982252,
"hom_count_reference_population": 1,
"allele_count_reference_population": 322,
"gnomad_exomes_af": 0.000115135,
"gnomad_genomes_af": 0.00101136,
"gnomad_exomes_ac": 168,
"gnomad_genomes_ac": 154,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005233854055404663,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.107,
"revel_prediction": "Benign",
"alphamissense_score": 0.087,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.911,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_012232.6",
"gene_symbol": "CAVIN1",
"hgnc_id": 9688,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000723360.1",
"gene_symbol": "ENSG00000294400",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.466G>A",
"hgvs_p": null
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "XR_934763.2",
"gene_symbol": "LOC102725238",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-154G>A",
"hgvs_p": null
}
],
"clinvar_disease": "CAVIN1-related disorder,Congenital generalized lipodystrophy type 4,Monogenic diabetes,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "Monogenic diabetes|not provided|Congenital generalized lipodystrophy type 4|not specified|CAVIN1-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}