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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: 1-53197050-A-AGC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=53197050&ref=A&alt=AGC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 53197050,
"ref": "A",
"alt": "AGC",
"effect": "frameshift_variant",
"transcript": "NM_000098.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "NM_000098.3",
"protein_id": "NP_000089.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 658,
"cds_start": 112,
"cds_end": null,
"cds_length": 1977,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000371486.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000098.3"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "ENST00000371486.4",
"protein_id": "ENSP00000360541.3",
"transcript_support_level": 1,
"aa_start": 38,
"aa_end": null,
"aa_length": 658,
"cds_start": 112,
"cds_end": null,
"cds_length": 1977,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000098.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371486.4"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "ENST00000873097.1",
"protein_id": "ENSP00000543156.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 680,
"cds_start": 112,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873097.1"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "ENST00000637252.1",
"protein_id": "ENSP00000490492.1",
"transcript_support_level": 5,
"aa_start": 38,
"aa_end": null,
"aa_length": 670,
"cds_start": 112,
"cds_end": null,
"cds_length": 2013,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000637252.1"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "ENST00000635862.1",
"protein_id": "ENSP00000490867.1",
"transcript_support_level": 5,
"aa_start": 38,
"aa_end": null,
"aa_length": 647,
"cds_start": 112,
"cds_end": null,
"cds_length": 1944,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635862.1"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "NM_001330589.2",
"protein_id": "NP_001317518.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 635,
"cds_start": 112,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330589.2"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "ENST00000636867.1",
"protein_id": "ENSP00000489631.1",
"transcript_support_level": 5,
"aa_start": 38,
"aa_end": null,
"aa_length": 635,
"cds_start": 112,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000636867.1"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "ENST00000948452.1",
"protein_id": "ENSP00000618511.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 631,
"cds_start": 112,
"cds_end": null,
"cds_length": 1896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948452.1"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "ENST00000873098.1",
"protein_id": "ENSP00000543157.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 608,
"cds_start": 112,
"cds_end": null,
"cds_length": 1827,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873098.1"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "ENST00000636891.1",
"protein_id": "ENSP00000490399.1",
"transcript_support_level": 5,
"aa_start": 38,
"aa_end": null,
"aa_length": 598,
"cds_start": 112,
"cds_end": null,
"cds_length": 1797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000636891.1"
},
{
"aa_ref": "S",
"aa_alt": "A?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs",
"transcript": "ENST00000636935.1",
"protein_id": "ENSP00000489757.1",
"transcript_support_level": 5,
"aa_start": 38,
"aa_end": null,
"aa_length": 223,
"cds_start": 112,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000636935.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.195_196dupGC",
"hgvs_p": null,
"transcript": "ENST00000468572.2",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000468572.2"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.110_111dupGC",
"hgvs_p": null,
"transcript": "ENST00000635888.1",
"protein_id": "ENSP00000490042.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000635888.1"
},
{
"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": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.110_111dupGC",
"hgvs_p": null,
"transcript": "ENST00000636239.1",
"protein_id": "ENSP00000490066.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000636239.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.110_111dupGC",
"hgvs_p": null,
"transcript": "ENST00000638135.1",
"protein_id": "ENSP00000489756.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000638135.1"
}
],
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"dbsnp": "rs754363068",
"frequency_reference_population": 0.000014945721,
"hom_count_reference_population": 0,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.0000151423,
"gnomad_genomes_af": 0.0000131529,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.097,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000098.3",
"gene_symbol": "CPT2",
"hgnc_id": 2330,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.110_111dupGC",
"hgvs_p": "p.Ser38fs"
}
],
"clinvar_disease": " 4, acute, infection-induced, myopathic form, neonatal form, severe infantile form, susceptibility to,Carnitine palmitoyl transferase II deficiency,Carnitine palmitoyltransferase II deficiency,Encephalopathy,Inborn genetic diseases,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:1",
"phenotype_combined": "Carnitine palmitoyl transferase II deficiency, myopathic form|Carnitine palmitoyl transferase II deficiency, severe infantile form|Carnitine palmitoyl transferase II deficiency, neonatal form|Carnitine palmitoyltransferase II deficiency|not provided|Encephalopathy, acute, infection-induced, susceptibility to, 4|Encephalopathy, acute, infection-induced, susceptibility to, 4;Carnitine palmitoyl transferase II deficiency, severe infantile form;Carnitine palmitoyl transferase II deficiency, myopathic form;Carnitine palmitoyl transferase II deficiency, neonatal form|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}