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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: 5-83483564-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=83483564&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 83483564,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_004385.5",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "NM_004385.5",
"protein_id": "NP_004376.2",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 3396,
"cds_start": 46,
"cds_end": null,
"cds_length": 10191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000265077.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004385.5"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "ENST00000265077.8",
"protein_id": "ENSP00000265077.3",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 3396,
"cds_start": 46,
"cds_end": null,
"cds_length": 10191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004385.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265077.8"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "ENST00000343200.9",
"protein_id": "ENSP00000340062.5",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 2409,
"cds_start": 46,
"cds_end": null,
"cds_length": 7230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000343200.9"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "ENST00000342785.8",
"protein_id": "ENSP00000342768.4",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 1642,
"cds_start": 46,
"cds_end": null,
"cds_length": 4929,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000342785.8"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "ENST00000513960.5",
"protein_id": "ENSP00000426251.1",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 1239,
"cds_start": 46,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513960.5"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "ENST00000502527.2",
"protein_id": "ENSP00000421362.2",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 655,
"cds_start": 46,
"cds_end": null,
"cds_length": 1968,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502527.2"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "ENST00000513984.5",
"protein_id": "ENSP00000426715.1",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 354,
"cds_start": 46,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513984.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.-99A>G",
"hgvs_p": null,
"transcript": "ENST00000512590.6",
"protein_id": "ENSP00000425959.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1594,
"cds_start": null,
"cds_end": null,
"cds_length": 4785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512590.6"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "NM_001164097.2",
"protein_id": "NP_001157569.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 2409,
"cds_start": 46,
"cds_end": null,
"cds_length": 7230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164097.2"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "NM_001164098.2",
"protein_id": "NP_001157570.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 1642,
"cds_start": 46,
"cds_end": null,
"cds_length": 4929,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164098.2"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val",
"transcript": "NM_001126336.3",
"protein_id": "NP_001119808.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 655,
"cds_start": 46,
"cds_end": null,
"cds_length": 1968,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001126336.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "n.458A>G",
"hgvs_p": null,
"transcript": "ENST00000503923.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000503923.1"
}
],
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"dbsnp": "rs573332559",
"frequency_reference_population": 0.0000013687212,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136872,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05440777540206909,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.027,
"revel_prediction": "Benign",
"alphamissense_score": 0.0762,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.36,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_004385.5",
"gene_symbol": "VCAN",
"hgnc_id": 2464,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.46A>G",
"hgvs_p": "p.Ile16Val"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}