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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: 19-10829208-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=10829208&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 10829208,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000389253.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2231T>C",
"hgvs_p": "p.Val744Ala",
"transcript": "NM_001005361.3",
"protein_id": "NP_001005361.1",
"transcript_support_level": null,
"aa_start": 744,
"aa_end": null,
"aa_length": 870,
"cds_start": 2231,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 2395,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": "ENST00000389253.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2231T>C",
"hgvs_p": "p.Val744Ala",
"transcript": "ENST00000389253.9",
"protein_id": "ENSP00000373905.4",
"transcript_support_level": 5,
"aa_start": 744,
"aa_end": null,
"aa_length": 870,
"cds_start": 2231,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 2395,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": "NM_001005361.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2231T>C",
"hgvs_p": "p.Val744Ala",
"transcript": "ENST00000355667.11",
"protein_id": "ENSP00000347890.6",
"transcript_support_level": 1,
"aa_start": 744,
"aa_end": null,
"aa_length": 870,
"cds_start": 2231,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 2395,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2231T>C",
"hgvs_p": "p.Val744Ala",
"transcript": "ENST00000585892.5",
"protein_id": "ENSP00000468734.1",
"transcript_support_level": 1,
"aa_start": 744,
"aa_end": null,
"aa_length": 869,
"cds_start": 2231,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 2395,
"cdna_end": null,
"cdna_length": 2774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2219T>C",
"hgvs_p": "p.Val740Ala",
"transcript": "ENST00000359692.10",
"protein_id": "ENSP00000352721.6",
"transcript_support_level": 1,
"aa_start": 740,
"aa_end": null,
"aa_length": 866,
"cds_start": 2219,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2369,
"cdna_end": null,
"cdna_length": 3588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2231T>C",
"hgvs_p": "p.Val744Ala",
"transcript": "NM_001005360.3",
"protein_id": "NP_001005360.1",
"transcript_support_level": null,
"aa_start": 744,
"aa_end": null,
"aa_length": 870,
"cds_start": 2231,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 2395,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2231T>C",
"hgvs_p": "p.Val744Ala",
"transcript": "NM_001190716.2",
"protein_id": "NP_001177645.1",
"transcript_support_level": null,
"aa_start": 744,
"aa_end": null,
"aa_length": 869,
"cds_start": 2231,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 2395,
"cdna_end": null,
"cdna_length": 3630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2219T>C",
"hgvs_p": "p.Val740Ala",
"transcript": "NM_001005362.3",
"protein_id": "NP_001005362.1",
"transcript_support_level": null,
"aa_start": 740,
"aa_end": null,
"aa_length": 866,
"cds_start": 2219,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2383,
"cdna_end": null,
"cdna_length": 3621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2219T>C",
"hgvs_p": "p.Val740Ala",
"transcript": "NM_004945.4",
"protein_id": "NP_004936.2",
"transcript_support_level": null,
"aa_start": 740,
"aa_end": null,
"aa_length": 866,
"cds_start": 2219,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2383,
"cdna_end": null,
"cdna_length": 3621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.2219T>C",
"hgvs_p": "p.Val740Ala",
"transcript": "ENST00000408974.8",
"protein_id": "ENSP00000386192.3",
"transcript_support_level": 2,
"aa_start": 740,
"aa_end": null,
"aa_length": 866,
"cds_start": 2219,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2254,
"cdna_end": null,
"cdna_length": 3013,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "c.95T>C",
"hgvs_p": "p.Val32Ala",
"transcript": "ENST00000589106.1",
"protein_id": "ENSP00000466914.1",
"transcript_support_level": 2,
"aa_start": 32,
"aa_end": null,
"aa_length": 136,
"cds_start": 95,
"cds_end": null,
"cds_length": 411,
"cdna_start": 97,
"cdna_end": null,
"cdna_length": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "n.4419T>C",
"hgvs_p": null,
"transcript": "ENST00000590806.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "n.1014T>C",
"hgvs_p": null,
"transcript": "ENST00000593203.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2507,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"hgvs_c": "n.1662T>C",
"hgvs_p": null,
"transcript": "ENST00000681972.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6793",
"gene_hgnc_id": 50251,
"hgvs_c": "n.*173T>C",
"hgvs_p": null,
"transcript": "ENST00000612376.1",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 63,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6793",
"gene_hgnc_id": 50251,
"hgvs_c": "n.*173T>C",
"hgvs_p": null,
"transcript": "NR_106851.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 63,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6793",
"gene_hgnc_id": 50251,
"hgvs_c": "n.*209T>C",
"hgvs_p": null,
"transcript": "unassigned_transcript_3223",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 22,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6793",
"gene_hgnc_id": 50251,
"hgvs_c": "n.*173T>C",
"hgvs_p": null,
"transcript": "unassigned_transcript_3224",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 20,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNM2",
"gene_hgnc_id": 2974,
"dbsnp": "rs777609224",
"frequency_reference_population": 0.000050190974,
"hom_count_reference_population": 0,
"allele_count_reference_population": 81,
"gnomad_exomes_af": 0.0000499439,
"gnomad_genomes_af": 0.0000525638,
"gnomad_exomes_ac": 73,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.15464046597480774,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.392,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2075,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.008,
"phylop100way_prediction": "Uncertain_significance",
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000389253.9",
"gene_symbol": "DNM2",
"hgnc_id": 2974,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2231T>C",
"hgvs_p": "p.Val744Ala"
},
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NR_106851.1",
"gene_symbol": "MIR6793",
"hgnc_id": 50251,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*173T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Charcot-Marie-Tooth disease dominant intermediate B,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Charcot-Marie-Tooth disease dominant intermediate B|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}