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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: 6-46711566-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=46711566&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 46711566,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000274793.12",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G7",
"gene_hgnc_id": 9040,
"hgvs_c": "c.593T>A",
"hgvs_p": "p.Ile198Lys",
"transcript": "NM_005084.4",
"protein_id": "NP_005075.3",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 441,
"cds_start": 593,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 823,
"cdna_end": null,
"cdna_length": 1915,
"mane_select": "ENST00000274793.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G7",
"gene_hgnc_id": 9040,
"hgvs_c": "c.593T>A",
"hgvs_p": "p.Ile198Lys",
"transcript": "ENST00000274793.12",
"protein_id": "ENSP00000274793.7",
"transcript_support_level": 1,
"aa_start": 198,
"aa_end": null,
"aa_length": 441,
"cds_start": 593,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 823,
"cdna_end": null,
"cdna_length": 1915,
"mane_select": "NM_005084.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G7",
"gene_hgnc_id": 9040,
"hgvs_c": "c.593T>A",
"hgvs_p": "p.Ile198Lys",
"transcript": "ENST00000537365.1",
"protein_id": "ENSP00000445666.1",
"transcript_support_level": 1,
"aa_start": 198,
"aa_end": null,
"aa_length": 441,
"cds_start": 593,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 771,
"cdna_end": null,
"cdna_length": 1747,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G7",
"gene_hgnc_id": 9040,
"hgvs_c": "c.593T>A",
"hgvs_p": "p.Ile198Lys",
"transcript": "NM_001168357.2",
"protein_id": "NP_001161829.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 441,
"cds_start": 593,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 1891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G7",
"gene_hgnc_id": 9040,
"hgvs_c": "c.593T>A",
"hgvs_p": "p.Ile198Lys",
"transcript": "XM_005249408.5",
"protein_id": "XP_005249465.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 441,
"cds_start": 593,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 731,
"cdna_end": null,
"cdna_length": 1823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G7",
"gene_hgnc_id": 9040,
"hgvs_c": "c.458T>A",
"hgvs_p": "p.Ile153Lys",
"transcript": "XM_047419359.1",
"protein_id": "XP_047275315.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 396,
"cds_start": 458,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 588,
"cdna_end": null,
"cdna_length": 1680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA2G7",
"gene_hgnc_id": 9040,
"hgvs_c": "c.593T>A",
"hgvs_p": "p.Ile198Lys",
"transcript": "XM_047419360.1",
"protein_id": "XP_047275316.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 272,
"cds_start": 593,
"cds_end": null,
"cds_length": 819,
"cdna_start": 823,
"cdna_end": null,
"cdna_length": 1165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PLA2G7",
"gene_hgnc_id": 9040,
"dbsnp": "rs1805018",
"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": 0.03421962261199951,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.042,
"revel_prediction": "Benign",
"alphamissense_score": 0.067,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.095,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000274793.12",
"gene_symbol": "PLA2G7",
"hgnc_id": 9040,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.593T>A",
"hgvs_p": "p.Ile198Lys"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}