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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: 6-31625522-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31625522&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 31625522,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004638.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRC2A",
"gene_hgnc_id": 13918,
"hgvs_c": "c.670A>C",
"hgvs_p": "p.Lys224Gln",
"transcript": "NM_004638.4",
"protein_id": "NP_004629.3",
"transcript_support_level": null,
"aa_start": 224,
"aa_end": null,
"aa_length": 2157,
"cds_start": 670,
"cds_end": null,
"cds_length": 6474,
"cdna_start": 914,
"cdna_end": null,
"cdna_length": 6903,
"mane_select": "ENST00000376033.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRC2A",
"gene_hgnc_id": 13918,
"hgvs_c": "c.670A>C",
"hgvs_p": "p.Lys224Gln",
"transcript": "ENST00000376033.3",
"protein_id": "ENSP00000365201.2",
"transcript_support_level": 1,
"aa_start": 224,
"aa_end": null,
"aa_length": 2157,
"cds_start": 670,
"cds_end": null,
"cds_length": 6474,
"cdna_start": 914,
"cdna_end": null,
"cdna_length": 6903,
"mane_select": "NM_004638.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRC2A",
"gene_hgnc_id": 13918,
"hgvs_c": "c.670A>C",
"hgvs_p": "p.Lys224Gln",
"transcript": "ENST00000376007.8",
"protein_id": "ENSP00000365175.4",
"transcript_support_level": 1,
"aa_start": 224,
"aa_end": null,
"aa_length": 2157,
"cds_start": 670,
"cds_end": null,
"cds_length": 6474,
"cdna_start": 872,
"cdna_end": null,
"cdna_length": 6861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRC2A",
"gene_hgnc_id": 13918,
"hgvs_c": "c.670A>C",
"hgvs_p": "p.Lys224Gln",
"transcript": "NM_080686.3",
"protein_id": "NP_542417.2",
"transcript_support_level": null,
"aa_start": 224,
"aa_end": null,
"aa_length": 2157,
"cds_start": 670,
"cds_end": null,
"cds_length": 6474,
"cdna_start": 877,
"cdna_end": null,
"cdna_length": 6866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRC2A",
"gene_hgnc_id": 13918,
"hgvs_c": "c.670A>C",
"hgvs_p": "p.Lys224Gln",
"transcript": "XM_047419336.1",
"protein_id": "XP_047275292.1",
"transcript_support_level": null,
"aa_start": 224,
"aa_end": null,
"aa_length": 2086,
"cds_start": 670,
"cds_end": null,
"cds_length": 6261,
"cdna_start": 877,
"cdna_end": null,
"cdna_length": 6653,
"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": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRC2A",
"gene_hgnc_id": 13918,
"hgvs_c": "n.515A>C",
"hgvs_p": null,
"transcript": "ENST00000469577.5",
"protein_id": null,
"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": 918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289282",
"gene_hgnc_id": null,
"hgvs_c": "c.*23A>C",
"hgvs_p": null,
"transcript": "ENST00000687518.1",
"protein_id": "ENSP00000509222.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 130,
"cds_start": -4,
"cds_end": null,
"cds_length": 393,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "PRRC2A",
"gene_hgnc_id": 13918,
"hgvs_c": "n.-232A>C",
"hgvs_p": null,
"transcript": "ENST00000464890.1",
"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": 593,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRC2A",
"gene_hgnc_id": 13918,
"hgvs_c": "n.*25A>C",
"hgvs_p": null,
"transcript": "ENST00000464079.1",
"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": 451,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRRC2A",
"gene_hgnc_id": 13918,
"dbsnp": "rs1251790288",
"frequency_reference_population": 6.997979e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.99798e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.30372077226638794,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.107,
"revel_prediction": "Benign",
"alphamissense_score": 0.1689,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.966,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004638.4",
"gene_symbol": "PRRC2A",
"hgnc_id": 13918,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.670A>C",
"hgvs_p": "p.Lys224Gln"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000687518.1",
"gene_symbol": "ENSG00000289282",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*23A>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}