← Back to variant description
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: 1-53197040-CA-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=53197040&ref=CA&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 53197040,
"ref": "CA",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "ENST00000371486.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": null,
"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.98delA",
"hgvs_p": "p.Gln33fs",
"transcript": "NM_000098.3",
"protein_id": "NP_000089.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 658,
"cds_start": 98,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 218,
"cdna_end": null,
"cdna_length": 2699,
"mane_select": "ENST00000371486.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": null,
"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.98delA",
"hgvs_p": "p.Gln33fs",
"transcript": "ENST00000371486.4",
"protein_id": "ENSP00000360541.3",
"transcript_support_level": 1,
"aa_start": 33,
"aa_end": null,
"aa_length": 658,
"cds_start": 98,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 218,
"cdna_end": null,
"cdna_length": 2699,
"mane_select": "NM_000098.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": null,
"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.98delA",
"hgvs_p": "p.Gln33fs",
"transcript": "ENST00000637252.1",
"protein_id": "ENSP00000490492.1",
"transcript_support_level": 5,
"aa_start": 33,
"aa_end": null,
"aa_length": 670,
"cds_start": 98,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 242,
"cdna_end": null,
"cdna_length": 2739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": null,
"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.98delA",
"hgvs_p": "p.Gln33fs",
"transcript": "ENST00000635862.1",
"protein_id": "ENSP00000490867.1",
"transcript_support_level": 5,
"aa_start": 33,
"aa_end": null,
"aa_length": 647,
"cds_start": 98,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 222,
"cdna_end": null,
"cdna_length": 2319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": null,
"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.98delA",
"hgvs_p": "p.Gln33fs",
"transcript": "NM_001330589.2",
"protein_id": "NP_001317518.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 635,
"cds_start": 98,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 218,
"cdna_end": null,
"cdna_length": 2630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": null,
"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.98delA",
"hgvs_p": "p.Gln33fs",
"transcript": "ENST00000636867.1",
"protein_id": "ENSP00000489631.1",
"transcript_support_level": 5,
"aa_start": 33,
"aa_end": null,
"aa_length": 635,
"cds_start": 98,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 2643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": null,
"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.98delA",
"hgvs_p": "p.Gln33fs",
"transcript": "ENST00000636891.1",
"protein_id": "ENSP00000490399.1",
"transcript_support_level": 5,
"aa_start": 33,
"aa_end": null,
"aa_length": 598,
"cds_start": 98,
"cds_end": null,
"cds_length": 1797,
"cdna_start": 242,
"cdna_end": null,
"cdna_length": 2746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": null,
"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.98delA",
"hgvs_p": "p.Gln33fs",
"transcript": "ENST00000636935.1",
"protein_id": "ENSP00000489757.1",
"transcript_support_level": 5,
"aa_start": 33,
"aa_end": null,
"aa_length": 223,
"cds_start": 98,
"cds_end": null,
"cds_length": 672,
"cdna_start": 229,
"cdna_end": null,
"cdna_length": 803,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.183delA",
"hgvs_p": null,
"transcript": "ENST00000468572.2",
"protein_id": null,
"transcript_support_level": 2,
"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": 772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.98delA",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.98delA",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.98delA",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"dbsnp": "rs917744011",
"frequency_reference_population": 0.000010400768,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000649265,
"gnomad_genomes_af": 0.0000460024,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 7,
"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": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.846,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000371486.4",
"gene_symbol": "CPT2",
"hgnc_id": 2330,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.98delA",
"hgvs_p": "p.Gln33fs"
}
],
"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,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8",
"phenotype_combined": "Carnitine palmitoyltransferase II deficiency|Carnitine palmitoyl transferase II deficiency, severe infantile form|not provided|Carnitine palmitoyl transferase II deficiency, severe infantile form;Carnitine palmitoyl transferase II deficiency, neonatal form|Carnitine palmitoyl transferase II deficiency, severe infantile form;Carnitine palmitoyl transferase II deficiency, myopathic form;Encephalopathy, acute, infection-induced, susceptibility to, 4;Carnitine palmitoyl transferase II deficiency, neonatal form|Encephalopathy, acute, infection-induced, susceptibility to, 4",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}