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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: 3-47562688-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=47562688&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 47562688,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001206943.2",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.1532T>A",
"hgvs_p": "p.Ile511Asn",
"transcript": "NM_006574.4",
"protein_id": "NP_006565.2",
"transcript_support_level": null,
"aa_start": 511,
"aa_end": null,
"aa_length": 539,
"cds_start": 1532,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264723.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006574.4"
},
{
"aa_ref": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.1532T>A",
"hgvs_p": "p.Ile511Asn",
"transcript": "ENST00000264723.9",
"protein_id": "ENSP00000264723.4",
"transcript_support_level": 1,
"aa_start": 511,
"aa_end": null,
"aa_length": 539,
"cds_start": 1532,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006574.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264723.9"
},
{
"aa_ref": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.1613T>A",
"hgvs_p": "p.Ile538Asn",
"transcript": "ENST00000383738.6",
"protein_id": "ENSP00000373244.2",
"transcript_support_level": 1,
"aa_start": 538,
"aa_end": null,
"aa_length": 566,
"cds_start": 1613,
"cds_end": null,
"cds_length": 1701,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000383738.6"
},
{
"aa_ref": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.1118T>A",
"hgvs_p": "p.Ile373Asn",
"transcript": "ENST00000456150.5",
"protein_id": "ENSP00000392096.1",
"transcript_support_level": 1,
"aa_start": 373,
"aa_end": null,
"aa_length": 401,
"cds_start": 1118,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000456150.5"
},
{
"aa_ref": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.1613T>A",
"hgvs_p": "p.Ile538Asn",
"transcript": "NM_001206943.2",
"protein_id": "NP_001193872.1",
"transcript_support_level": null,
"aa_start": 538,
"aa_end": null,
"aa_length": 566,
"cds_start": 1613,
"cds_end": null,
"cds_length": 1701,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206943.2"
},
{
"aa_ref": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.1199T>A",
"hgvs_p": "p.Ile400Asn",
"transcript": "NM_001206945.2",
"protein_id": "NP_001193874.1",
"transcript_support_level": null,
"aa_start": 400,
"aa_end": null,
"aa_length": 428,
"cds_start": 1199,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206945.2"
},
{
"aa_ref": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.1118T>A",
"hgvs_p": "p.Ile373Asn",
"transcript": "NM_001206942.2",
"protein_id": "NP_001193871.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 401,
"cds_start": 1118,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206942.2"
},
{
"aa_ref": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.1118T>A",
"hgvs_p": "p.Ile373Asn",
"transcript": "XM_047447332.1",
"protein_id": "XP_047303288.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 401,
"cds_start": 1118,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447332.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.*22T>A",
"hgvs_p": null,
"transcript": "NM_001206944.2",
"protein_id": "NP_001193873.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 477,
"cds_start": null,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206944.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"hgvs_c": "c.*22T>A",
"hgvs_p": null,
"transcript": "ENST00000610462.1",
"protein_id": "ENSP00000478923.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 477,
"cds_start": null,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000610462.1"
}
],
"gene_symbol": "CSPG5",
"gene_hgnc_id": 2467,
"dbsnp": "rs773841687",
"frequency_reference_population": 0.00002479387,
"hom_count_reference_population": 0,
"allele_count_reference_population": 40,
"gnomad_exomes_af": 0.000025998,
"gnomad_genomes_af": 0.0000131881,
"gnomad_exomes_ac": 38,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5910823345184326,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.255,
"revel_prediction": "Benign",
"alphamissense_score": 0.7027,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.804,
"phylop100way_prediction": "Pathogenic",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_001206943.2",
"gene_symbol": "CSPG5",
"hgnc_id": 2467,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1613T>A",
"hgvs_p": "p.Ile538Asn"
}
],
"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
}