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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: 3-189973934-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=189973934&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 189973934,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_018192.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"hgvs_c": "c.1523G>T",
"hgvs_p": "p.Gly508Val",
"transcript": "NM_018192.4",
"protein_id": "NP_060662.2",
"transcript_support_level": null,
"aa_start": 508,
"aa_end": null,
"aa_length": 708,
"cds_start": 1523,
"cds_end": null,
"cds_length": 2127,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000319332.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018192.4"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"hgvs_c": "c.1523G>T",
"hgvs_p": "p.Gly508Val",
"transcript": "ENST00000319332.10",
"protein_id": "ENSP00000316881.5",
"transcript_support_level": 1,
"aa_start": 508,
"aa_end": null,
"aa_length": 708,
"cds_start": 1523,
"cds_end": null,
"cds_length": 2127,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018192.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000319332.10"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"hgvs_c": "c.980G>T",
"hgvs_p": "p.Gly327Val",
"transcript": "ENST00000427335.6",
"protein_id": "ENSP00000408947.2",
"transcript_support_level": 1,
"aa_start": 327,
"aa_end": null,
"aa_length": 527,
"cds_start": 980,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427335.6"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"hgvs_c": "c.1592G>T",
"hgvs_p": "p.Gly531Val",
"transcript": "ENST00000895815.1",
"protein_id": "ENSP00000565874.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 731,
"cds_start": 1592,
"cds_end": null,
"cds_length": 2196,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000895815.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"hgvs_c": "c.1520G>T",
"hgvs_p": "p.Gly507Val",
"transcript": "ENST00000895814.1",
"protein_id": "ENSP00000565873.1",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 707,
"cds_start": 1520,
"cds_end": null,
"cds_length": 2124,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000895814.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"hgvs_c": "c.1451G>T",
"hgvs_p": "p.Gly484Val",
"transcript": "ENST00000943436.1",
"protein_id": "ENSP00000613495.1",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 684,
"cds_start": 1451,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943436.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"hgvs_c": "c.1523G>T",
"hgvs_p": "p.Gly508Val",
"transcript": "ENST00000895816.1",
"protein_id": "ENSP00000565875.1",
"transcript_support_level": null,
"aa_start": 508,
"aa_end": null,
"aa_length": 661,
"cds_start": 1523,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000895816.1"
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"hgvs_c": "c.980G>T",
"hgvs_p": "p.Gly327Val",
"transcript": "NM_001134418.2",
"protein_id": "NP_001127890.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 527,
"cds_start": 980,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001134418.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"hgvs_c": "n.257G>T",
"hgvs_p": null,
"transcript": "ENST00000482780.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000482780.1"
}
],
"gene_symbol": "P3H2",
"gene_hgnc_id": 19317,
"dbsnp": "rs724159988",
"frequency_reference_population": 0.0000018587084,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 6.84107e-7,
"gnomad_genomes_af": 0.0000131351,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9124066829681396,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.68,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9834,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.25,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.379,
"phylop100way_prediction": "Uncertain_significance",
"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": "Pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_018192.4",
"gene_symbol": "P3H2",
"hgnc_id": 19317,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1523G>T",
"hgvs_p": "p.Gly508Val"
}
],
"clinvar_disease": " high, with cataract and vitreoretinal degeneration,Myopia",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Myopia, high, with cataract and vitreoretinal degeneration",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}