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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: 1-45511415-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=45511415&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 45511415,
"ref": "C",
"alt": "A",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "ENST00000319248.13",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMACHC",
"gene_hgnc_id": 24525,
"hgvs_c": "c.*2200C>A",
"hgvs_p": null,
"transcript": "NM_015506.3",
"protein_id": "NP_056321.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 282,
"cds_start": -4,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5049,
"mane_select": "ENST00000401061.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMACHC",
"gene_hgnc_id": 24525,
"hgvs_c": "c.*2200C>A",
"hgvs_p": null,
"transcript": "ENST00000401061.9",
"protein_id": "ENSP00000383840.4",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 282,
"cds_start": -4,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5049,
"mane_select": "NM_015506.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.515-1G>T",
"hgvs_p": null,
"transcript": "NM_181697.3",
"protein_id": "NP_859048.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": -4,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 945,
"mane_select": "ENST00000319248.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.515-1G>T",
"hgvs_p": null,
"transcript": "ENST00000319248.13",
"protein_id": "ENSP00000361152.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": -4,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 945,
"mane_select": "NM_181697.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMACHC",
"gene_hgnc_id": 24525,
"hgvs_c": "c.*2200C>A",
"hgvs_p": null,
"transcript": "NM_001330540.2",
"protein_id": "NP_001317469.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 225,
"cds_start": -4,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.515-1G>T",
"hgvs_p": null,
"transcript": "NM_001202431.2",
"protein_id": "NP_001189360.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": -4,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.515-1G>T",
"hgvs_p": null,
"transcript": "NM_002574.4",
"protein_id": "NP_002565.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": -4,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.515-1G>T",
"hgvs_p": null,
"transcript": "NM_181696.3",
"protein_id": "NP_859047.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": -4,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1139,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.515-1G>T",
"hgvs_p": null,
"transcript": "ENST00000262746.5",
"protein_id": "ENSP00000262746.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": -4,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.515-1G>T",
"hgvs_p": null,
"transcript": "ENST00000424390.2",
"protein_id": "ENSP00000389047.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": -4,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1296,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.515-1G>T",
"hgvs_p": null,
"transcript": "ENST00000447184.6",
"protein_id": "ENSP00000407034.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": -4,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.515-1G>T",
"hgvs_p": null,
"transcript": "ENST00000676549.1",
"protein_id": "ENSP00000503140.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": -4,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1082,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"hgvs_c": "c.209-1G>T",
"hgvs_p": null,
"transcript": "ENST00000372079.1",
"protein_id": "ENSP00000361150.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 97,
"cds_start": -4,
"cds_end": null,
"cds_length": 294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 609,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRDX1",
"gene_hgnc_id": 9352,
"dbsnp": "rs751828470",
"frequency_reference_population": 0.00002877197,
"hom_count_reference_population": 0,
"allele_count_reference_population": 42,
"gnomad_exomes_af": 0.000028772,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 42,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3499999940395355,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9240000247955322,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.874,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.99,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999988247793601,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000319248.13",
"gene_symbol": "PRDX1",
"hgnc_id": 9352,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.515-1G>T",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000401061.9",
"gene_symbol": "MMACHC",
"hgnc_id": 24525,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*2200C>A",
"hgvs_p": null
}
],
"clinvar_disease": " DIGENIC, cblC TYPE,Cobalamin C disease,METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblC TYPE, DIGENIC|Cobalamin C disease|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}