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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: 6-106105508-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=106105508&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 106105508,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000369096.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1348C>T",
"hgvs_p": "p.Leu450Phe",
"transcript": "NM_001198.4",
"protein_id": "NP_001189.2",
"transcript_support_level": null,
"aa_start": 450,
"aa_end": null,
"aa_length": 825,
"cds_start": 1348,
"cds_end": null,
"cds_length": 2478,
"cdna_start": 1566,
"cdna_end": null,
"cdna_length": 5148,
"mane_select": "ENST00000369096.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1348C>T",
"hgvs_p": "p.Leu450Phe",
"transcript": "ENST00000369096.9",
"protein_id": "ENSP00000358092.4",
"transcript_support_level": 1,
"aa_start": 450,
"aa_end": null,
"aa_length": 825,
"cds_start": 1348,
"cds_end": null,
"cds_length": 2478,
"cdna_start": 1566,
"cdna_end": null,
"cdna_length": 5148,
"mane_select": "NM_001198.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1240C>T",
"hgvs_p": "p.Leu414Phe",
"transcript": "ENST00000369091.6",
"protein_id": "ENSP00000358087.2",
"transcript_support_level": 1,
"aa_start": 414,
"aa_end": null,
"aa_length": 789,
"cds_start": 1240,
"cds_end": null,
"cds_length": 2370,
"cdna_start": 1460,
"cdna_end": null,
"cdna_length": 2612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.946C>T",
"hgvs_p": "p.Leu316Phe",
"transcript": "ENST00000369089.3",
"protein_id": "ENSP00000358085.3",
"transcript_support_level": 1,
"aa_start": 316,
"aa_end": null,
"aa_length": 691,
"cds_start": 946,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 1092,
"cdna_end": null,
"cdna_length": 4675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1390C>T",
"hgvs_p": "p.Leu464Phe",
"transcript": "ENST00000648754.1",
"protein_id": "ENSP00000498029.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 839,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 1650,
"cdna_end": null,
"cdna_length": 3576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1240C>T",
"hgvs_p": "p.Leu414Phe",
"transcript": "ENST00000651185.1",
"protein_id": "ENSP00000498716.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 789,
"cds_start": 1240,
"cds_end": null,
"cds_length": 2370,
"cdna_start": 1487,
"cdna_end": null,
"cdna_length": 5070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1240C>T",
"hgvs_p": "p.Leu414Phe",
"transcript": "ENST00000652320.1",
"protein_id": "ENSP00000498580.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 789,
"cds_start": 1240,
"cds_end": null,
"cds_length": 2370,
"cdna_start": 1483,
"cdna_end": null,
"cdna_length": 5066,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.946C>T",
"hgvs_p": "p.Leu316Phe",
"transcript": "NM_182907.3",
"protein_id": "NP_878911.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 691,
"cds_start": 946,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 1091,
"cdna_end": null,
"cdna_length": 4673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1390C>T",
"hgvs_p": "p.Leu464Phe",
"transcript": "XM_011536062.4",
"protein_id": "XP_011534364.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 839,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 1483,
"cdna_end": null,
"cdna_length": 5065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1390C>T",
"hgvs_p": "p.Leu464Phe",
"transcript": "XM_006715550.4",
"protein_id": "XP_006715613.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 796,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2391,
"cdna_start": 1483,
"cdna_end": null,
"cdna_length": 4936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1240C>T",
"hgvs_p": "p.Leu414Phe",
"transcript": "XM_017011187.2",
"protein_id": "XP_016866676.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 789,
"cds_start": 1240,
"cds_end": null,
"cds_length": 2370,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 5017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1240C>T",
"hgvs_p": "p.Leu414Phe",
"transcript": "XM_047419246.1",
"protein_id": "XP_047275202.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 789,
"cds_start": 1240,
"cds_end": null,
"cds_length": 2370,
"cdna_start": 1597,
"cdna_end": null,
"cdna_length": 5179,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.1348C>T",
"hgvs_p": "p.Leu450Phe",
"transcript": "XM_047419247.1",
"protein_id": "XP_047275203.1",
"transcript_support_level": null,
"aa_start": 450,
"aa_end": null,
"aa_length": 782,
"cds_start": 1348,
"cds_end": null,
"cds_length": 2349,
"cdna_start": 1566,
"cdna_end": null,
"cdna_length": 5019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.874C>T",
"hgvs_p": "p.Leu292Phe",
"transcript": "XM_011536064.4",
"protein_id": "XP_011534366.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 667,
"cds_start": 874,
"cds_end": null,
"cds_length": 2004,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 4644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"hgvs_c": "c.946C>T",
"hgvs_p": "p.Leu316Phe",
"transcript": "XM_047419248.1",
"protein_id": "XP_047275204.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 648,
"cds_start": 946,
"cds_end": null,
"cds_length": 1947,
"cdna_start": 1091,
"cdna_end": null,
"cdna_length": 4544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.458-58683G>A",
"hgvs_p": null,
"transcript": "ENST00000636437.1",
"protein_id": "ENSP00000490376.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": -4,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2261,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "n.458-27193G>A",
"hgvs_p": null,
"transcript": "ENST00000636335.1",
"protein_id": "ENSP00000490221.1",
"transcript_support_level": 5,
"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": 1219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRDM1",
"gene_hgnc_id": 9346,
"dbsnp": "rs141465160",
"frequency_reference_population": 0.0031444319,
"hom_count_reference_population": 43,
"allele_count_reference_population": 5075,
"gnomad_exomes_af": 0.00302259,
"gnomad_genomes_af": 0.00431368,
"gnomad_exomes_ac": 4418,
"gnomad_genomes_ac": 657,
"gnomad_exomes_homalt": 39,
"gnomad_genomes_homalt": 4,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00593075156211853,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.1372,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.048,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000369096.9",
"gene_symbol": "PRDM1",
"hgnc_id": 9346,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1348C>T",
"hgvs_p": "p.Leu450Phe"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000636335.1",
"gene_symbol": "ATG5",
"hgnc_id": 589,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.458-27193G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1 O:1",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}