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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: 2-88691804-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=88691804&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 88691804,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_144563.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPIA",
"gene_hgnc_id": 10297,
"hgvs_c": "c.106C>A",
"hgvs_p": "p.Leu36Ile",
"transcript": "NM_144563.3",
"protein_id": "NP_653164.2",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 311,
"cds_start": 106,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000283646.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_144563.3"
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPIA",
"gene_hgnc_id": 10297,
"hgvs_c": "c.106C>A",
"hgvs_p": "p.Leu36Ile",
"transcript": "ENST00000283646.5",
"protein_id": "ENSP00000283646.3",
"transcript_support_level": 1,
"aa_start": 36,
"aa_end": null,
"aa_length": 311,
"cds_start": 106,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_144563.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000283646.5"
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPIA",
"gene_hgnc_id": 10297,
"hgvs_c": "c.106C>A",
"hgvs_p": "p.Leu36Ile",
"transcript": "ENST00000871060.1",
"protein_id": "ENSP00000541119.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 293,
"cds_start": 106,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871060.1"
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPIA",
"gene_hgnc_id": 10297,
"hgvs_c": "c.106C>A",
"hgvs_p": "p.Leu36Ile",
"transcript": "ENST00000871058.1",
"protein_id": "ENSP00000541117.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 291,
"cds_start": 106,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871058.1"
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPIA",
"gene_hgnc_id": 10297,
"hgvs_c": "c.106C>A",
"hgvs_p": "p.Leu36Ile",
"transcript": "ENST00000871059.1",
"protein_id": "ENSP00000541118.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 272,
"cds_start": 106,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871059.1"
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPIA",
"gene_hgnc_id": 10297,
"hgvs_c": "c.106C>A",
"hgvs_p": "p.Leu36Ile",
"transcript": "ENST00000915183.1",
"protein_id": "ENSP00000585242.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 270,
"cds_start": 106,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915183.1"
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPIA",
"gene_hgnc_id": 10297,
"hgvs_c": "c.106C>A",
"hgvs_p": "p.Leu36Ile",
"transcript": "ENST00000915184.1",
"protein_id": "ENSP00000585243.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 250,
"cds_start": 106,
"cds_end": null,
"cds_length": 753,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915184.1"
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPIA",
"gene_hgnc_id": 10297,
"hgvs_c": "c.106C>A",
"hgvs_p": "p.Leu36Ile",
"transcript": "XM_047443733.1",
"protein_id": "XP_047299689.1",
"transcript_support_level": null,
"aa_start": 36,
"aa_end": null,
"aa_length": 180,
"cds_start": 106,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443733.1"
}
],
"gene_symbol": "RPIA",
"gene_hgnc_id": 10297,
"dbsnp": "rs201777997",
"frequency_reference_population": 0.0003128244,
"hom_count_reference_population": 4,
"allele_count_reference_population": 499,
"gnomad_exomes_af": 0.000173272,
"gnomad_genomes_af": 0.00163467,
"gnomad_exomes_ac": 250,
"gnomad_genomes_ac": 249,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006114602088928223,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.153,
"revel_prediction": "Benign",
"alphamissense_score": 0.0699,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.664,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_144563.3",
"gene_symbol": "RPIA",
"hgnc_id": 10297,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.106C>A",
"hgvs_p": "p.Leu36Ile"
}
],
"clinvar_disease": "Inborn genetic diseases,RPIA-related disorder,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "not provided|Inborn genetic diseases|RPIA-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}