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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: 19-40396017-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40396017&ref=C&alt=T&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": "PRX",
"hgnc_id": 13797,
"hgvs_c": "c.2620G>A",
"hgvs_p": "p.Ala874Thr",
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_001411127.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 4,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0767,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.6,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Charcot-Marie-Tooth disease type 4,Peripheral neuropathy",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.09436404705047607,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1461,
"aa_ref": "A",
"aa_start": 779,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4867,
"cdna_start": 2618,
"cds_end": null,
"cds_length": 4386,
"cds_start": 2335,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_181882.3",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.2335G>A",
"hgvs_p": "p.Ala779Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000324001.8",
"protein_coding": true,
"protein_id": "NP_870998.2",
"strand": false,
"transcript": "NM_181882.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1461,
"aa_ref": "A",
"aa_start": 779,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4867,
"cdna_start": 2618,
"cds_end": null,
"cds_length": 4386,
"cds_start": 2335,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000324001.8",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.2335G>A",
"hgvs_p": "p.Ala779Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_181882.3",
"protein_coding": true,
"protein_id": "ENSP00000326018.6",
"strand": false,
"transcript": "ENST00000324001.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 147,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5502,
"cdna_start": null,
"cds_end": null,
"cds_length": 444,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000291825.11",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.*2540G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000291825.6",
"strand": false,
"transcript": "ENST00000291825.11",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1556,
"aa_ref": "A",
"aa_start": 874,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4916,
"cdna_start": 2667,
"cds_end": null,
"cds_length": 4671,
"cds_start": 2620,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001411127.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.2620G>A",
"hgvs_p": "p.Ala874Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001398056.1",
"strand": false,
"transcript": "NM_001411127.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1556,
"aa_ref": "A",
"aa_start": 874,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4920,
"cdna_start": 2671,
"cds_end": null,
"cds_length": 4671,
"cds_start": 2620,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000674005.2",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.2620G>A",
"hgvs_p": "p.Ala874Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501261.1",
"strand": false,
"transcript": "ENST00000674005.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1461,
"aa_ref": "A",
"aa_start": 779,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4907,
"cdna_start": 2660,
"cds_end": null,
"cds_length": 4386,
"cds_start": 2335,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000903445.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.2335G>A",
"hgvs_p": "p.Ala779Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000573504.1",
"strand": false,
"transcript": "ENST00000903445.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1461,
"aa_ref": "A",
"aa_start": 779,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4880,
"cdna_start": 2629,
"cds_end": null,
"cds_length": 4386,
"cds_start": 2335,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000903446.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.2335G>A",
"hgvs_p": "p.Ala779Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000573505.1",
"strand": false,
"transcript": "ENST00000903446.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1414,
"aa_ref": "A",
"aa_start": 732,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4447,
"cdna_start": 2196,
"cds_end": null,
"cds_length": 4245,
"cds_start": 2194,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000676076.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.2194G>A",
"hgvs_p": "p.Ala732Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502166.1",
"strand": false,
"transcript": "ENST00000676076.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1322,
"aa_ref": "A",
"aa_start": 640,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4985,
"cdna_start": 2734,
"cds_end": null,
"cds_length": 3969,
"cds_start": 1918,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000673881.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.1918G>A",
"hgvs_p": "p.Ala640Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501070.1",
"strand": false,
"transcript": "ENST00000673881.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1322,
"aa_ref": "A",
"aa_start": 640,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4433,
"cdna_start": 2184,
"cds_end": null,
"cds_length": 3969,
"cds_start": 1918,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000674773.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.1918G>A",
"hgvs_p": "p.Ala640Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502579.1",
"strand": false,
"transcript": "ENST00000674773.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1269,
"aa_ref": "A",
"aa_start": 587,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4298,
"cdna_start": 2045,
"cds_end": null,
"cds_length": 3810,
"cds_start": 1759,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000903447.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.1759G>A",
"hgvs_p": "p.Ala587Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000573506.1",
"strand": false,
"transcript": "ENST00000903447.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1427,
"aa_ref": "A",
"aa_start": 745,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4553,
"cdna_start": 2304,
"cds_end": null,
"cds_length": 4284,
"cds_start": 2233,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017027047.2",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.2233G>A",
"hgvs_p": "p.Ala745Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882536.1",
"strand": false,
"transcript": "XM_017027047.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 147,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5506,
"cdna_start": null,
"cds_end": null,
"cds_length": 444,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_020956.2",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.*2540G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_066007.1",
"strand": false,
"transcript": "NM_020956.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 96,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4473,
"cdna_start": null,
"cds_end": null,
"cds_length": 291,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000676316.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.*1929G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501881.1",
"strand": false,
"transcript": "ENST00000676316.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 92,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4261,
"cdna_start": null,
"cds_end": null,
"cds_length": 279,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000675517.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "c.*1929G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501865.1",
"strand": false,
"transcript": "ENST00000675517.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4348,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000676260.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "n.*2085G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502436.1",
"strand": false,
"transcript": "ENST00000676260.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4348,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000676260.1",
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"hgvs_c": "n.*2085G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502436.1",
"strand": false,
"transcript": "ENST00000676260.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs369505684",
"effect": "missense_variant",
"frequency_reference_population": 0.0000027365209,
"gene_hgnc_id": 13797,
"gene_symbol": "PRX",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000273652,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": "Peripheral neuropathy|Charcot-Marie-Tooth disease type 4",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.299,
"pos": 40396017,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.102,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001411127.1"
}
]
}