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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: 1-39897382-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=39897382&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 39897382,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000372816.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYCL",
"gene_hgnc_id": 7555,
"hgvs_c": "c.1085C>G",
"hgvs_p": "p.Thr362Ser",
"transcript": "NM_001033081.3",
"protein_id": "NP_001028253.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 364,
"cds_start": 1085,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 1568,
"cdna_end": null,
"cdna_length": 3522,
"mane_select": "ENST00000372816.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYCL",
"gene_hgnc_id": 7555,
"hgvs_c": "c.1085C>G",
"hgvs_p": "p.Thr362Ser",
"transcript": "ENST00000372816.3",
"protein_id": "ENSP00000361903.2",
"transcript_support_level": 2,
"aa_start": 362,
"aa_end": null,
"aa_length": 364,
"cds_start": 1085,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 1568,
"cdna_end": null,
"cdna_length": 3522,
"mane_select": "NM_001033081.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYCL",
"gene_hgnc_id": 7555,
"hgvs_c": "c.1175C>G",
"hgvs_p": "p.Thr392Ser",
"transcript": "ENST00000397332.3",
"protein_id": "ENSP00000380494.2",
"transcript_support_level": 1,
"aa_start": 392,
"aa_end": null,
"aa_length": 394,
"cds_start": 1175,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 3158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYCL",
"gene_hgnc_id": 7555,
"hgvs_c": "c.1175C>G",
"hgvs_p": "p.Thr392Ser",
"transcript": "NM_001033082.3",
"protein_id": "NP_001028254.2",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 394,
"cds_start": 1175,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 3158,
"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": "MYCL-AS1",
"gene_hgnc_id": 40386,
"hgvs_c": "n.50G>C",
"hgvs_p": null,
"transcript": "ENST00000837552.1",
"protein_id": null,
"transcript_support_level": null,
"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": 836,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYCL-AS1",
"gene_hgnc_id": 40386,
"hgvs_c": "n.50G>C",
"hgvs_p": null,
"transcript": "ENST00000837554.1",
"protein_id": null,
"transcript_support_level": null,
"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": 633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MYCL-AS1",
"gene_hgnc_id": 40386,
"hgvs_c": "n.326-361G>C",
"hgvs_p": null,
"transcript": "ENST00000418255.2",
"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": 1112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MYCL-AS1",
"gene_hgnc_id": 40386,
"hgvs_c": "n.304-361G>C",
"hgvs_p": null,
"transcript": "ENST00000837551.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1095,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MYCL-AS1",
"gene_hgnc_id": 40386,
"hgvs_c": "n.273-361G>C",
"hgvs_p": null,
"transcript": "NR_183424.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MYCL-AS1",
"gene_hgnc_id": 40386,
"hgvs_c": "n.36-361G>C",
"hgvs_p": null,
"transcript": "NR_183425.1",
"protein_id": null,
"transcript_support_level": null,
"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": 822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MYCL",
"gene_hgnc_id": 7555,
"dbsnp": "rs3134614",
"frequency_reference_population": 0.880818,
"hom_count_reference_population": 620979,
"allele_count_reference_population": 1407031,
"gnomad_exomes_af": 0.877815,
"gnomad_genomes_af": 0.909311,
"gnomad_exomes_ac": 1268532,
"gnomad_genomes_ac": 138499,
"gnomad_exomes_homalt": 557770,
"gnomad_genomes_homalt": 63209,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 5.394342110776051e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.207,
"revel_prediction": "Benign",
"alphamissense_score": 0.0587,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.284,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000372816.3",
"gene_symbol": "MYCL",
"hgnc_id": 7555,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1085C>G",
"hgvs_p": "p.Thr362Ser"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000837552.1",
"gene_symbol": "MYCL-AS1",
"hgnc_id": 40386,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.50G>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}