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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: 1-53213590-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=53213590&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 53213590,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000098.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1972A>C",
"hgvs_p": "p.Ser658Arg",
"transcript": "NM_000098.3",
"protein_id": "NP_000089.1",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 658,
"cds_start": 1972,
"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": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1972A>C",
"hgvs_p": "p.Ser658Arg",
"transcript": "ENST00000371486.4",
"protein_id": "ENSP00000360541.3",
"transcript_support_level": 1,
"aa_start": 658,
"aa_end": null,
"aa_length": 658,
"cds_start": 1972,
"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": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.2038A>C",
"hgvs_p": "p.Ser680Arg",
"transcript": "ENST00000873097.1",
"protein_id": "ENSP00000543156.1",
"transcript_support_level": null,
"aa_start": 680,
"aa_end": null,
"aa_length": 680,
"cds_start": 2038,
"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": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.2008A>C",
"hgvs_p": "p.Ser670Arg",
"transcript": "ENST00000637252.1",
"protein_id": "ENSP00000490492.1",
"transcript_support_level": 5,
"aa_start": 670,
"aa_end": null,
"aa_length": 670,
"cds_start": 2008,
"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": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1939A>C",
"hgvs_p": "p.Ser647Arg",
"transcript": "ENST00000635862.1",
"protein_id": "ENSP00000490867.1",
"transcript_support_level": 5,
"aa_start": 647,
"aa_end": null,
"aa_length": 647,
"cds_start": 1939,
"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": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1903A>C",
"hgvs_p": "p.Ser635Arg",
"transcript": "NM_001330589.2",
"protein_id": "NP_001317518.1",
"transcript_support_level": null,
"aa_start": 635,
"aa_end": null,
"aa_length": 635,
"cds_start": 1903,
"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": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1903A>C",
"hgvs_p": "p.Ser635Arg",
"transcript": "ENST00000636867.1",
"protein_id": "ENSP00000489631.1",
"transcript_support_level": 5,
"aa_start": 635,
"aa_end": null,
"aa_length": 635,
"cds_start": 1903,
"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": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1891A>C",
"hgvs_p": "p.Ser631Arg",
"transcript": "ENST00000948452.1",
"protein_id": "ENSP00000618511.1",
"transcript_support_level": null,
"aa_start": 631,
"aa_end": null,
"aa_length": 631,
"cds_start": 1891,
"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": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.1822A>C",
"hgvs_p": "p.Ser608Arg",
"transcript": "ENST00000873098.1",
"protein_id": "ENSP00000543157.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 608,
"cds_start": 1822,
"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": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.667A>C",
"hgvs_p": "p.Ser223Arg",
"transcript": "ENST00000636935.1",
"protein_id": "ENSP00000489757.1",
"transcript_support_level": 5,
"aa_start": 223,
"aa_end": null,
"aa_length": 223,
"cds_start": 667,
"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": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "c.*225A>C",
"hgvs_p": null,
"transcript": "ENST00000636891.1",
"protein_id": "ENSP00000490399.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 598,
"cds_start": null,
"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": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236723",
"gene_hgnc_id": null,
"hgvs_c": "n.186T>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": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*1958A>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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*1619A>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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*1619A>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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*1958A>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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*1619A>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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPT2",
"gene_hgnc_id": 2330,
"hgvs_c": "n.*1619A>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": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236723",
"gene_hgnc_id": null,
"hgvs_c": "n.-118T>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": "rs1553170037",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.13760793209075928,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.173,
"revel_prediction": "Benign",
"alphamissense_score": 0.1518,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.191,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000098.3",
"gene_symbol": "CPT2",
"hgnc_id": 2330,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.1972A>C",
"hgvs_p": "p.Ser658Arg"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000452466.1",
"gene_symbol": "ENSG00000236723",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.186T>G",
"hgvs_p": null
}
],
"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",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:7",
"phenotype_combined": "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;Encephalopathy, acute, infection-induced, susceptibility to, 4|Carnitine palmitoyl transferase II deficiency, myopathic form|Carnitine palmitoyl transferase II deficiency, neonatal form|Encephalopathy, acute, infection-induced, susceptibility to, 4|Inborn genetic diseases|Carnitine palmitoyl transferase II deficiency, severe infantile form",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}