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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: 1-2304323-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=2304323&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 2304323,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000378536.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKI",
"gene_hgnc_id": 10896,
"hgvs_c": "c.1505C>A",
"hgvs_p": "p.Pro502Gln",
"transcript": "NM_003036.4",
"protein_id": "NP_003027.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 728,
"cds_start": 1505,
"cds_end": null,
"cds_length": 2187,
"cdna_start": 1953,
"cdna_end": null,
"cdna_length": 6083,
"mane_select": "ENST00000378536.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKI",
"gene_hgnc_id": 10896,
"hgvs_c": "c.1505C>A",
"hgvs_p": "p.Pro502Gln",
"transcript": "ENST00000378536.5",
"protein_id": "ENSP00000367797.4",
"transcript_support_level": 1,
"aa_start": 502,
"aa_end": null,
"aa_length": 728,
"cds_start": 1505,
"cds_end": null,
"cds_length": 2187,
"cdna_start": 1953,
"cdna_end": null,
"cdna_length": 6083,
"mane_select": "NM_003036.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKI",
"gene_hgnc_id": 10896,
"hgvs_c": "c.1511C>A",
"hgvs_p": "p.Pro504Gln",
"transcript": "XM_005244775.4",
"protein_id": "XP_005244832.1",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 730,
"cds_start": 1511,
"cds_end": null,
"cds_length": 2193,
"cdna_start": 1959,
"cdna_end": null,
"cdna_length": 6089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKI",
"gene_hgnc_id": 10896,
"hgvs_c": "c.1019C>A",
"hgvs_p": "p.Pro340Gln",
"transcript": "XM_017002128.2",
"protein_id": "XP_016857617.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 566,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 1381,
"cdna_end": null,
"cdna_length": 5511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKI",
"gene_hgnc_id": 10896,
"hgvs_c": "c.641C>A",
"hgvs_p": "p.Pro214Gln",
"transcript": "XM_005244776.5",
"protein_id": "XP_005244833.1",
"transcript_support_level": null,
"aa_start": 214,
"aa_end": null,
"aa_length": 440,
"cds_start": 641,
"cds_end": null,
"cds_length": 1323,
"cdna_start": 9891,
"cdna_end": null,
"cdna_length": 14021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKI",
"gene_hgnc_id": 10896,
"hgvs_c": "c.635C>A",
"hgvs_p": "p.Pro212Gln",
"transcript": "XM_047428466.1",
"protein_id": "XP_047284422.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 438,
"cds_start": 635,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 9885,
"cdna_end": null,
"cdna_length": 14015,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SKI",
"gene_hgnc_id": 10896,
"hgvs_c": "n.494C>A",
"hgvs_p": null,
"transcript": "ENST00000507179.1",
"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": 539,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SKI",
"gene_hgnc_id": 10896,
"dbsnp": "rs1057520161",
"frequency_reference_population": 7.146124e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.14612e-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": 0.5591033697128296,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9800000190734863,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": 0.552,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8378,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.515,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.98,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000378536.5",
"gene_symbol": "SKI",
"hgnc_id": 10896,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1505C>A",
"hgvs_p": "p.Pro502Gln"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}