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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: 22-36265988-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=36265988&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 36265988,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000397278.8",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1152T>G",
"hgvs_p": "p.Ile384Met",
"transcript": "NM_003661.4",
"protein_id": "NP_003652.2",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 398,
"cds_start": 1152,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 1258,
"cdna_end": null,
"cdna_length": 2795,
"mane_select": "ENST00000397278.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1152T>G",
"hgvs_p": "p.Ile384Met",
"transcript": "ENST00000397278.8",
"protein_id": "ENSP00000380448.4",
"transcript_support_level": 1,
"aa_start": 384,
"aa_end": null,
"aa_length": 398,
"cds_start": 1152,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 1258,
"cdna_end": null,
"cdna_length": 2795,
"mane_select": "NM_003661.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1200T>G",
"hgvs_p": "p.Ile400Met",
"transcript": "ENST00000319136.8",
"protein_id": "ENSP00000317674.4",
"transcript_support_level": 1,
"aa_start": 400,
"aa_end": null,
"aa_length": 414,
"cds_start": 1200,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 1467,
"cdna_end": null,
"cdna_length": 3000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1239T>G",
"hgvs_p": "p.Ile413Met",
"transcript": "ENST00000438034.6",
"protein_id": "ENSP00000404525.2",
"transcript_support_level": 4,
"aa_start": 413,
"aa_end": null,
"aa_length": 427,
"cds_start": 1239,
"cds_end": null,
"cds_length": 1284,
"cdna_start": 1451,
"cdna_end": null,
"cdna_length": 2984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1200T>G",
"hgvs_p": "p.Ile400Met",
"transcript": "NM_145343.3",
"protein_id": "NP_663318.1",
"transcript_support_level": null,
"aa_start": 400,
"aa_end": null,
"aa_length": 414,
"cds_start": 1200,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 1412,
"cdna_end": null,
"cdna_length": 2949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1152T>G",
"hgvs_p": "p.Ile384Met",
"transcript": "NM_001136540.2",
"protein_id": "NP_001130012.1",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 398,
"cds_start": 1152,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 1297,
"cdna_end": null,
"cdna_length": 2834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1152T>G",
"hgvs_p": "p.Ile384Met",
"transcript": "ENST00000427990.6",
"protein_id": "ENSP00000391302.2",
"transcript_support_level": 3,
"aa_start": 384,
"aa_end": null,
"aa_length": 398,
"cds_start": 1152,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 1297,
"cdna_end": null,
"cdna_length": 2830,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1098T>G",
"hgvs_p": "p.Ile366Met",
"transcript": "NM_001136541.2",
"protein_id": "NP_001130013.1",
"transcript_support_level": null,
"aa_start": 366,
"aa_end": null,
"aa_length": 380,
"cds_start": 1098,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 2741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1098T>G",
"hgvs_p": "p.Ile366Met",
"transcript": "NM_001362927.2",
"protein_id": "NP_001349856.1",
"transcript_support_level": null,
"aa_start": 366,
"aa_end": null,
"aa_length": 380,
"cds_start": 1098,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 1243,
"cdna_end": null,
"cdna_length": 2780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "c.1098T>G",
"hgvs_p": "p.Ile366Met",
"transcript": "ENST00000426053.5",
"protein_id": "ENSP00000388477.1",
"transcript_support_level": 2,
"aa_start": 366,
"aa_end": null,
"aa_length": 380,
"cds_start": 1098,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 2808,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "n.*914T>G",
"hgvs_p": null,
"transcript": "ENST00000433768.6",
"protein_id": "ENSP00000392514.1",
"transcript_support_level": 4,
"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": 2990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"hgvs_c": "n.*914T>G",
"hgvs_p": null,
"transcript": "ENST00000433768.6",
"protein_id": "ENSP00000392514.1",
"transcript_support_level": 4,
"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": 2990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "APOL1",
"gene_hgnc_id": 618,
"dbsnp": "rs60910145",
"frequency_reference_population": 0.011181926,
"hom_count_reference_population": 2103,
"allele_count_reference_population": 18029,
"gnomad_exomes_af": 0.00595298,
"gnomad_genomes_af": 0.0617676,
"gnomad_exomes_ac": 8699,
"gnomad_genomes_ac": 9330,
"gnomad_exomes_homalt": 1043,
"gnomad_genomes_homalt": 1060,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008493423461914062,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.1048,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.623,
"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": "ENST00000397278.8",
"gene_symbol": "APOL1",
"hgnc_id": 618,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1152T>G",
"hgvs_p": "p.Ile384Met"
}
],
"clinvar_disease": " Segmental Glomerular, susceptibility to,APOL1-associated kidney disease,Focal segmental glomerulosclerosis,Focal segmental glomerulosclerosis 4,Glomerulonephritis,Hyalinosis,Nephrotic range proteinuria,Proteinuria,Sickled erythrocytes,Steroid-resistant nephrotic syndrome,not provided,not specified",
"clinvar_classification": " risk factor,Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1 B:4 O:1",
"phenotype_combined": "Hyalinosis, Segmental Glomerular|not provided|Nephrotic range proteinuria|Glomerulonephritis|not specified|Proteinuria|Focal segmental glomerulosclerosis|Steroid-resistant nephrotic syndrome;Focal segmental glomerulosclerosis|Focal segmental glomerulosclerosis;Sickled erythrocytes|Focal segmental glomerulosclerosis 4, susceptibility to|APOL1-associated kidney disease",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity; risk factor",
"custom_annotations": null
}
],
"message": null
}