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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: 5-32786283-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=32786283&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 32786283,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000265074.13",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.1564A>G",
"hgvs_p": "p.Asn522Asp",
"transcript": "NM_001204375.2",
"protein_id": "NP_001191304.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 541,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 2020,
"cdna_end": null,
"cdna_length": 7457,
"mane_select": "ENST00000265074.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.1564A>G",
"hgvs_p": "p.Asn522Asp",
"transcript": "ENST00000265074.13",
"protein_id": "ENSP00000265074.8",
"transcript_support_level": 1,
"aa_start": 522,
"aa_end": null,
"aa_length": 541,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 2020,
"cdna_end": null,
"cdna_length": 7457,
"mane_select": "NM_001204375.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.1561A>G",
"hgvs_p": "p.Asn521Asp",
"transcript": "ENST00000415167.2",
"protein_id": "ENSP00000398028.2",
"transcript_support_level": 1,
"aa_start": 521,
"aa_end": null,
"aa_length": 540,
"cds_start": 1561,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1615,
"cdna_end": null,
"cdna_length": 1753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.1561A>G",
"hgvs_p": "p.Asn521Asp",
"transcript": "NM_000908.4",
"protein_id": "NP_000899.1",
"transcript_support_level": null,
"aa_start": 521,
"aa_end": null,
"aa_length": 540,
"cds_start": 1561,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 2017,
"cdna_end": null,
"cdna_length": 7454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.916A>G",
"hgvs_p": "p.Asn306Asp",
"transcript": "NM_001363652.2",
"protein_id": "NP_001350581.1",
"transcript_support_level": null,
"aa_start": 306,
"aa_end": null,
"aa_length": 325,
"cds_start": 916,
"cds_end": null,
"cds_length": 978,
"cdna_start": 930,
"cdna_end": null,
"cdna_length": 6367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.916A>G",
"hgvs_p": "p.Asn306Asp",
"transcript": "ENST00000434067.6",
"protein_id": "ENSP00000388408.2",
"transcript_support_level": 5,
"aa_start": 306,
"aa_end": null,
"aa_length": 325,
"cds_start": 916,
"cds_end": null,
"cds_length": 978,
"cdna_start": 2172,
"cdna_end": null,
"cdna_length": 2715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.913A>G",
"hgvs_p": "p.Asn305Asp",
"transcript": "NM_001204376.2",
"protein_id": "NP_001191305.1",
"transcript_support_level": null,
"aa_start": 305,
"aa_end": null,
"aa_length": 324,
"cds_start": 913,
"cds_end": null,
"cds_length": 975,
"cdna_start": 927,
"cdna_end": null,
"cdna_length": 6364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.913A>G",
"hgvs_p": "p.Asn305Asp",
"transcript": "ENST00000326958.5",
"protein_id": "ENSP00000318340.2",
"transcript_support_level": 2,
"aa_start": 305,
"aa_end": null,
"aa_length": 324,
"cds_start": 913,
"cds_end": null,
"cds_length": 975,
"cdna_start": 939,
"cdna_end": null,
"cdna_length": 6380,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.844A>G",
"hgvs_p": "p.Asn282Asp",
"transcript": "NM_001364458.2",
"protein_id": "NP_001351387.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 301,
"cds_start": 844,
"cds_end": null,
"cds_length": 906,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 6294,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"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": "NPR3",
"gene_hgnc_id": 7945,
"hgvs_c": "c.793A>G",
"hgvs_p": "p.Asn265Asp",
"transcript": "NM_001364460.2",
"protein_id": "NP_001351389.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 284,
"cds_start": 793,
"cds_end": null,
"cds_length": 855,
"cdna_start": 807,
"cdna_end": null,
"cdna_length": 6244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPR3",
"gene_hgnc_id": 7945,
"dbsnp": "rs2270915",
"frequency_reference_population": 0.2100262,
"hom_count_reference_population": 36640,
"allele_count_reference_population": 332101,
"gnomad_exomes_af": 0.212537,
"gnomad_genomes_af": 0.18645,
"gnomad_exomes_ac": 303721,
"gnomad_genomes_ac": 28380,
"gnomad_exomes_homalt": 33751,
"gnomad_genomes_homalt": 2889,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0012596547603607178,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.055,
"revel_prediction": "Benign",
"alphamissense_score": 0.0922,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.843,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000265074.13",
"gene_symbol": "NPR3",
"hgnc_id": 7945,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1564A>G",
"hgvs_p": "p.Asn522Asp"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}