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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: 12-39553926-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=39553926&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 39553926,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005164.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "c.2209G>A",
"hgvs_p": "p.Asp737Asn",
"transcript": "NM_005164.4",
"protein_id": "NP_005155.1",
"transcript_support_level": null,
"aa_start": 737,
"aa_end": null,
"aa_length": 740,
"cds_start": 2209,
"cds_end": null,
"cds_length": 2223,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000308666.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005164.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "c.2209G>A",
"hgvs_p": "p.Asp737Asn",
"transcript": "ENST00000308666.4",
"protein_id": "ENSP00000310688.3",
"transcript_support_level": 1,
"aa_start": 737,
"aa_end": null,
"aa_length": 740,
"cds_start": 2209,
"cds_end": null,
"cds_length": 2223,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005164.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000308666.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Asp730Asn",
"transcript": "ENST00000961978.1",
"protein_id": "ENSP00000632037.1",
"transcript_support_level": null,
"aa_start": 730,
"aa_end": null,
"aa_length": 733,
"cds_start": 2188,
"cds_end": null,
"cds_length": 2202,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961978.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "c.2083G>A",
"hgvs_p": "p.Asp695Asn",
"transcript": "NM_001412789.1",
"protein_id": "NP_001399718.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 698,
"cds_start": 2083,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001412789.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "c.2077G>A",
"hgvs_p": "p.Asp693Asn",
"transcript": "ENST00000961977.1",
"protein_id": "ENSP00000632036.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 696,
"cds_start": 2077,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961977.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "c.1912G>A",
"hgvs_p": "p.Asp638Asn",
"transcript": "NM_001412791.1",
"protein_id": "NP_001399720.1",
"transcript_support_level": null,
"aa_start": 638,
"aa_end": null,
"aa_length": 641,
"cds_start": 1912,
"cds_end": null,
"cds_length": 1926,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001412791.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "c.934G>A",
"hgvs_p": "p.Asp312Asn",
"transcript": "NM_001412793.1",
"protein_id": "NP_001399722.1",
"transcript_support_level": null,
"aa_start": 312,
"aa_end": null,
"aa_length": 315,
"cds_start": 934,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001412793.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "c.2003+19790G>A",
"hgvs_p": null,
"transcript": "XM_017018992.3",
"protein_id": "XP_016874481.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 674,
"cds_start": null,
"cds_end": null,
"cds_length": 2025,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018992.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "n.2517G>A",
"hgvs_p": null,
"transcript": "NR_182045.1",
"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": "NR_182045.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"hgvs_c": "n.2424G>A",
"hgvs_p": null,
"transcript": "NR_182046.1",
"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": "NR_182046.1"
}
],
"gene_symbol": "ABCD2",
"gene_hgnc_id": 66,
"dbsnp": "rs541565694",
"frequency_reference_population": 0.00003295073,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000329593,
"gnomad_genomes_af": 0.0000328684,
"gnomad_exomes_ac": 48,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08566257357597351,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.194,
"revel_prediction": "Benign",
"alphamissense_score": 0.0658,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.141,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_005164.4",
"gene_symbol": "ABCD2",
"hgnc_id": 66,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2209G>A",
"hgvs_p": "p.Asp737Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}