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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: 3-47576947-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=47576947&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CSPG5",
"hgnc_id": 2467,
"hgvs_c": "c.1079G>T",
"hgvs_p": "p.Arg360Leu",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_001206943.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": 0.4611,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.2,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.2597549259662628,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 539,
"aa_ref": "R",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2154,
"cdna_start": 1251,
"cds_end": null,
"cds_length": 1620,
"cds_start": 1079,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_006574.4",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.1079G>T",
"hgvs_p": "p.Arg360Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264723.9",
"protein_coding": true,
"protein_id": "NP_006565.2",
"strand": false,
"transcript": "NM_006574.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 539,
"aa_ref": "R",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2154,
"cdna_start": 1251,
"cds_end": null,
"cds_length": 1620,
"cds_start": 1079,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000264723.9",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.1079G>T",
"hgvs_p": "p.Arg360Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006574.4",
"protein_coding": true,
"protein_id": "ENSP00000264723.4",
"strand": false,
"transcript": "ENST00000264723.9",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 566,
"aa_ref": "R",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4161,
"cdna_start": 3178,
"cds_end": null,
"cds_length": 1701,
"cds_start": 1079,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000383738.6",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.1079G>T",
"hgvs_p": "p.Arg360Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000373244.2",
"strand": false,
"transcript": "ENST00000383738.6",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 401,
"aa_ref": "R",
"aa_start": 222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2089,
"cdna_start": 1187,
"cds_end": null,
"cds_length": 1206,
"cds_start": 665,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000456150.5",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.665G>T",
"hgvs_p": "p.Arg222Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000392096.1",
"strand": false,
"transcript": "ENST00000456150.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 566,
"aa_ref": "R",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2235,
"cdna_start": 1251,
"cds_end": null,
"cds_length": 1701,
"cds_start": 1079,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001206943.2",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.1079G>T",
"hgvs_p": "p.Arg360Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001193872.1",
"strand": false,
"transcript": "NM_001206943.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 477,
"aa_ref": "R",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2078,
"cdna_start": 1251,
"cds_end": null,
"cds_length": 1434,
"cds_start": 1079,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001206944.2",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.1079G>T",
"hgvs_p": "p.Arg360Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001193873.1",
"strand": false,
"transcript": "NM_001206944.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 477,
"aa_ref": "R",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2073,
"cdna_start": 1255,
"cds_end": null,
"cds_length": 1434,
"cds_start": 1079,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000610462.1",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.1079G>T",
"hgvs_p": "p.Arg360Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000478923.1",
"strand": false,
"transcript": "ENST00000610462.1",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 428,
"aa_ref": "R",
"aa_start": 222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2317,
"cdna_start": 1333,
"cds_end": null,
"cds_length": 1287,
"cds_start": 665,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001206945.2",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.665G>T",
"hgvs_p": "p.Arg222Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001193874.1",
"strand": false,
"transcript": "NM_001206945.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 401,
"aa_ref": "R",
"aa_start": 222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2236,
"cdna_start": 1333,
"cds_end": null,
"cds_length": 1206,
"cds_start": 665,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001206942.2",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.665G>T",
"hgvs_p": "p.Arg222Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001193871.1",
"strand": false,
"transcript": "NM_001206942.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 401,
"aa_ref": "R",
"aa_start": 222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2036,
"cdna_start": 1133,
"cds_end": null,
"cds_length": 1206,
"cds_start": 665,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047447332.1",
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"hgvs_c": "c.665G>T",
"hgvs_p": "p.Arg222Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047303288.1",
"strand": false,
"transcript": "XM_047447332.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201338850",
"effect": "missense_variant",
"frequency_reference_population": 0.0000037186564,
"gene_hgnc_id": 2467,
"gene_symbol": "CSPG5",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84356e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.000032839,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 3.859,
"pos": 47576947,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.128,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001206943.2"
}
]
}