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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: 6-31635190-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31635190&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRRC2A",
"hgnc_id": 13918,
"hgvs_c": "c.5219G>A",
"hgvs_p": "p.Arg1740His",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_004638.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BA1",
"acmg_score": -13,
"allele_count_reference_population": 578568,
"alphamissense_prediction": null,
"alphamissense_score": 0.0979,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.55,
"chr": "6",
"clinvar_classification": "Benign",
"clinvar_disease": "PRRC2A-related disorder",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0008297562599182129,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2157,
"aa_ref": "R",
"aa_start": 1740,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6903,
"cdna_start": 5463,
"cds_end": null,
"cds_length": 6474,
"cds_start": 5219,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "NM_004638.4",
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"hgvs_c": "c.5219G>A",
"hgvs_p": "p.Arg1740His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000376033.3",
"protein_coding": true,
"protein_id": "NP_004629.3",
"strand": true,
"transcript": "NM_004638.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2157,
"aa_ref": "R",
"aa_start": 1740,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6903,
"cdna_start": 5463,
"cds_end": null,
"cds_length": 6474,
"cds_start": 5219,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000376033.3",
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"hgvs_c": "c.5219G>A",
"hgvs_p": "p.Arg1740His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004638.4",
"protein_coding": true,
"protein_id": "ENSP00000365201.2",
"strand": true,
"transcript": "ENST00000376033.3",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2157,
"aa_ref": "R",
"aa_start": 1740,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6861,
"cdna_start": 5421,
"cds_end": null,
"cds_length": 6474,
"cds_start": 5219,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000376007.8",
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"hgvs_c": "c.5219G>A",
"hgvs_p": "p.Arg1740His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365175.4",
"strand": true,
"transcript": "ENST00000376007.8",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2157,
"aa_ref": "R",
"aa_start": 1740,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6866,
"cdna_start": 5426,
"cds_end": null,
"cds_length": 6474,
"cds_start": 5219,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "NM_080686.3",
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"hgvs_c": "c.5219G>A",
"hgvs_p": "p.Arg1740His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_542417.2",
"strand": true,
"transcript": "NM_080686.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2086,
"aa_ref": "R",
"aa_start": 1740,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6653,
"cdna_start": 5426,
"cds_end": null,
"cds_length": 6261,
"cds_start": 5219,
"consequences": [
"missense_variant"
],
"exon_count": 30,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_047419336.1",
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"hgvs_c": "c.5219G>A",
"hgvs_p": "p.Arg1740His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275292.1",
"strand": true,
"transcript": "XM_047419336.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 756,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000484787.1",
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"hgvs_c": "n.630G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000484787.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 347,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000469501.1",
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"hgvs_c": "n.-52G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000469501.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 732,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000487089.1",
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"hgvs_c": "n.-170G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000487089.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1071,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000487839.1",
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"hgvs_c": "n.-186G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000487839.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1046089",
"effect": "missense_variant",
"frequency_reference_population": 0.35849684,
"gene_hgnc_id": 13918,
"gene_symbol": "PRRC2A",
"gnomad_exomes_ac": 517868,
"gnomad_exomes_af": 0.354259,
"gnomad_exomes_homalt": 93991,
"gnomad_genomes_ac": 60700,
"gnomad_genomes_af": 0.399242,
"gnomad_genomes_homalt": 12571,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 106562,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "PRRC2A-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.406,
"pos": 31635190,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.155,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004638.4"
}
]
}