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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: 3-73062425-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=73062425&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 73062425,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_018029.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EBLN2",
"gene_hgnc_id": 25493,
"hgvs_c": "c.344A>G",
"hgvs_p": "p.His115Arg",
"transcript": "NM_018029.4",
"protein_id": "NP_060499.3",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 272,
"cds_start": 344,
"cds_end": null,
"cds_length": 819,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 1679,
"mane_select": "ENST00000533473.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EBLN2",
"gene_hgnc_id": 25493,
"hgvs_c": "c.344A>G",
"hgvs_p": "p.His115Arg",
"transcript": "ENST00000533473.1",
"protein_id": "ENSP00000432104.1",
"transcript_support_level": 6,
"aa_start": 115,
"aa_end": null,
"aa_length": 272,
"cds_start": 344,
"cds_end": null,
"cds_length": 819,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 1679,
"mane_select": "NM_018029.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PPP4R2",
"gene_hgnc_id": 18296,
"hgvs_c": "c.420-1248A>G",
"hgvs_p": null,
"transcript": "NM_174907.4",
"protein_id": "NP_777567.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 417,
"cds_start": -4,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4957,
"mane_select": "ENST00000356692.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PPP4R2",
"gene_hgnc_id": 18296,
"hgvs_c": "c.420-1248A>G",
"hgvs_p": null,
"transcript": "ENST00000356692.10",
"protein_id": "ENSP00000349124.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 417,
"cds_start": -4,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4957,
"mane_select": "NM_174907.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PPP4R2",
"gene_hgnc_id": 18296,
"hgvs_c": "c.525-1248A>G",
"hgvs_p": null,
"transcript": "ENST00000710398.1",
"protein_id": "ENSP00000518252.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 452,
"cds_start": -4,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4957,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PPP4R2",
"gene_hgnc_id": 18296,
"hgvs_c": "c.306-1248A>G",
"hgvs_p": null,
"transcript": "NM_001318026.2",
"protein_id": "NP_001304955.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 379,
"cds_start": -4,
"cds_end": null,
"cds_length": 1140,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PPP4R2",
"gene_hgnc_id": 18296,
"hgvs_c": "c.249-1248A>G",
"hgvs_p": null,
"transcript": "NM_001318025.2",
"protein_id": "NP_001304954.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 360,
"cds_start": -4,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PPP4R2",
"gene_hgnc_id": 18296,
"hgvs_c": "c.-32-1248A>G",
"hgvs_p": null,
"transcript": "NM_001318027.2",
"protein_id": "NP_001304956.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 246,
"cds_start": -4,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4724,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PPP4R2",
"gene_hgnc_id": 18296,
"hgvs_c": "c.419+1365A>G",
"hgvs_p": null,
"transcript": "ENST00000488810.5",
"protein_id": "ENSP00000418750.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 225,
"cds_start": -4,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PPP4R2",
"gene_hgnc_id": 18296,
"hgvs_c": "n.249-1248A>G",
"hgvs_p": null,
"transcript": "ENST00000482242.5",
"protein_id": "ENSP00000418568.1",
"transcript_support_level": 3,
"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": 771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EBLN2",
"gene_hgnc_id": 25493,
"dbsnp": "rs374990636",
"frequency_reference_population": 0.000024202076,
"hom_count_reference_population": 0,
"allele_count_reference_population": 39,
"gnomad_exomes_af": 0.0000226148,
"gnomad_genomes_af": 0.0000394187,
"gnomad_exomes_ac": 33,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03783291578292847,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.25,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.091,
"revel_prediction": "Benign",
"alphamissense_score": 0.1989,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.347,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.25,
"spliceai_max_prediction": "Uncertain_significance",
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018029.4",
"gene_symbol": "EBLN2",
"hgnc_id": 25493,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.344A>G",
"hgvs_p": "p.His115Arg"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_174907.4",
"gene_symbol": "PPP4R2",
"hgnc_id": 18296,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.420-1248A>G",
"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
}