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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: 1-53211016-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=53211016&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 53211016,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000098.3",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1342T>C",
"hgvs_p": "p.Phe448Leu",
"transcript": "NM_000098.3",
"protein_id": "NP_000089.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 658,
"cds_start": 1342,
"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": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1342T>C",
"hgvs_p": "p.Phe448Leu",
"transcript": "ENST00000371486.4",
"protein_id": "ENSP00000360541.3",
"transcript_support_level": 1,
"aa_start": 448,
"aa_end": null,
"aa_length": 658,
"cds_start": 1342,
"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": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1342T>C",
"hgvs_p": "p.Phe448Leu",
"transcript": "ENST00000873097.1",
"protein_id": "ENSP00000543156.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 680,
"cds_start": 1342,
"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": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1342T>C",
"hgvs_p": "p.Phe448Leu",
"transcript": "ENST00000637252.1",
"protein_id": "ENSP00000490492.1",
"transcript_support_level": 5,
"aa_start": 448,
"aa_end": null,
"aa_length": 670,
"cds_start": 1342,
"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": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1342T>C",
"hgvs_p": "p.Phe448Leu",
"transcript": "ENST00000635862.1",
"protein_id": "ENSP00000490867.1",
"transcript_support_level": 5,
"aa_start": 448,
"aa_end": null,
"aa_length": 647,
"cds_start": 1342,
"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": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1342T>C",
"hgvs_p": "p.Phe448Leu",
"transcript": "NM_001330589.2",
"protein_id": "NP_001317518.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 635,
"cds_start": 1342,
"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": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1342T>C",
"hgvs_p": "p.Phe448Leu",
"transcript": "ENST00000636867.1",
"protein_id": "ENSP00000489631.1",
"transcript_support_level": 5,
"aa_start": 448,
"aa_end": null,
"aa_length": 635,
"cds_start": 1342,
"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": "F",
"aa_alt": "L",
"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": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1261T>C",
"hgvs_p": "p.Phe421Leu",
"transcript": "ENST00000948452.1",
"protein_id": "ENSP00000618511.1",
"transcript_support_level": null,
"aa_start": 421,
"aa_end": null,
"aa_length": 631,
"cds_start": 1261,
"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": "F",
"aa_alt": "L",
"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": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1261T>C",
"hgvs_p": "p.Phe421Leu",
"transcript": "ENST00000873098.1",
"protein_id": "ENSP00000543157.1",
"transcript_support_level": null,
"aa_start": 421,
"aa_end": null,
"aa_length": 608,
"cds_start": 1261,
"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": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1342T>C",
"hgvs_p": "p.Phe448Leu",
"transcript": "ENST00000636891.1",
"protein_id": "ENSP00000490399.1",
"transcript_support_level": 5,
"aa_start": 448,
"aa_end": null,
"aa_length": 598,
"cds_start": 1342,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.341-2248T>C",
"hgvs_p": null,
"transcript": "ENST00000636935.1",
"protein_id": "ENSP00000489757.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 223,
"cds_start": null,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*1328T>C",
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*989T>C",
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.3542T>C",
"hgvs_p": null,
"transcript": "ENST00000637726.1",
"protein_id": null,
"transcript_support_level": 6,
"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": "ENST00000637726.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*989T>C",
"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"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*1328T>C",
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*989T>C",
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*989T>C",
"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"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236723",
"gene_hgnc_id": null,
"hgvs_c": "n.436-472A>G",
"hgvs_p": null,
"transcript": "ENST00000452466.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000452466.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236723",
"gene_hgnc_id": null,
"hgvs_c": "n.286-607A>G",
"hgvs_p": null,
"transcript": "ENST00000629810.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000629810.1"
}
],
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"dbsnp": "rs74315297",
"frequency_reference_population": 0.00011771586,
"hom_count_reference_population": 0,
"allele_count_reference_population": 190,
"gnomad_exomes_af": 0.000119024,
"gnomad_genomes_af": 0.00010515,
"gnomad_exomes_ac": 174,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7589259743690491,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.952,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9485,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.5,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.674,
"phylop100way_prediction": "Pathogenic",
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,BP6",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 1,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000098.3",
"gene_symbol": "CPT2",
"hgnc_id": 2330,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.1342T>C",
"hgvs_p": "p.Phe448Leu"
},
{
"score": 2,
"benign_score": 1,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000452466.1",
"gene_symbol": "ENSG00000236723",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.436-472A>G",
"hgvs_p": null
}
],
"clinvar_disease": " myopathic form, neonatal form, severe infantile form,Carnitine palmitoyl transferase II deficiency,Carnitine palmitoyltransferase II deficiency,not provided,not specified",
"clinvar_classification": " other,Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 B:1 O:2",
"phenotype_combined": "not specified|not provided|Carnitine palmitoyltransferase II deficiency|Carnitine palmitoyl transferase II deficiency, severe infantile form;Carnitine palmitoyl transferase II deficiency, myopathic form;Carnitine palmitoyl transferase II deficiency, neonatal form",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity; other",
"custom_annotations": null
}
],
"message": null
}