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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: 19-40398764-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40398764&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 40398764,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000324001.8",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.237C>T",
"hgvs_p": "p.Asp79Asp",
"transcript": "NM_181882.3",
"protein_id": "NP_870998.2",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 1461,
"cds_start": 237,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 4867,
"mane_select": "ENST00000324001.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.237C>T",
"hgvs_p": "p.Asp79Asp",
"transcript": "ENST00000324001.8",
"protein_id": "ENSP00000326018.6",
"transcript_support_level": 1,
"aa_start": 79,
"aa_end": null,
"aa_length": 1461,
"cds_start": 237,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 4867,
"mane_select": "NM_181882.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.237C>T",
"hgvs_p": "p.Asp79Asp",
"transcript": "ENST00000291825.11",
"protein_id": "ENSP00000291825.6",
"transcript_support_level": 1,
"aa_start": 79,
"aa_end": null,
"aa_length": 147,
"cds_start": 237,
"cds_end": null,
"cds_length": 444,
"cdna_start": 506,
"cdna_end": null,
"cdna_length": 5502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.-181C>T",
"hgvs_p": null,
"transcript": "ENST00000673881.1",
"protein_id": "ENSP00000501070.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1322,
"cds_start": -4,
"cds_end": null,
"cds_length": 3969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.522C>T",
"hgvs_p": "p.Asp174Asp",
"transcript": "NM_001411127.1",
"protein_id": "NP_001398056.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 1556,
"cds_start": 522,
"cds_end": null,
"cds_length": 4671,
"cdna_start": 569,
"cdna_end": null,
"cdna_length": 4916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.522C>T",
"hgvs_p": "p.Asp174Asp",
"transcript": "ENST00000674005.2",
"protein_id": "ENSP00000501261.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 1556,
"cds_start": 522,
"cds_end": null,
"cds_length": 4671,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 4920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Asp17Asp",
"transcript": "ENST00000676076.1",
"protein_id": "ENSP00000502166.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 1414,
"cds_start": 51,
"cds_end": null,
"cds_length": 4245,
"cdna_start": 53,
"cdna_end": null,
"cdna_length": 4447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.237C>T",
"hgvs_p": "p.Asp79Asp",
"transcript": "NM_020956.2",
"protein_id": "NP_066007.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 147,
"cds_start": 237,
"cds_end": null,
"cds_length": 444,
"cdna_start": 506,
"cdna_end": null,
"cdna_length": 5506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Asp17Asp",
"transcript": "ENST00000676316.1",
"protein_id": "ENSP00000501881.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 96,
"cds_start": 51,
"cds_end": null,
"cds_length": 291,
"cdna_start": 53,
"cdna_end": null,
"cdna_length": 4473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Asp17Asp",
"transcript": "ENST00000675517.1",
"protein_id": "ENSP00000501865.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 92,
"cds_start": 51,
"cds_end": null,
"cds_length": 279,
"cdna_start": 53,
"cdna_end": null,
"cdna_length": 4261,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.135C>T",
"hgvs_p": "p.Asp45Asp",
"transcript": "XM_017027047.2",
"protein_id": "XP_016882536.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 1427,
"cds_start": 135,
"cds_end": null,
"cds_length": 4284,
"cdna_start": 206,
"cdna_end": null,
"cdna_length": 4553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "n.154C>T",
"hgvs_p": null,
"transcript": "ENST00000674642.1",
"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": 298,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "n.284C>T",
"hgvs_p": null,
"transcript": "ENST00000674978.1",
"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": 428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "n.51C>T",
"hgvs_p": null,
"transcript": "ENST00000676260.1",
"protein_id": "ENSP00000502436.1",
"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": 4348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.-181C>T",
"hgvs_p": null,
"transcript": "ENST00000673881.1",
"protein_id": "ENSP00000501070.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1322,
"cds_start": -4,
"cds_end": null,
"cds_length": 3969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.-36-794C>T",
"hgvs_p": null,
"transcript": "ENST00000674773.1",
"protein_id": "ENSP00000502579.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1322,
"cds_start": -4,
"cds_end": null,
"cds_length": 3969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4433,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.158-55C>T",
"hgvs_p": null,
"transcript": "ENST00000675300.1",
"protein_id": "ENSP00000502008.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 81,
"cds_start": -4,
"cds_end": null,
"cds_length": 247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 247,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"dbsnp": "rs376174896",
"frequency_reference_population": 0.00003779177,
"hom_count_reference_population": 0,
"allele_count_reference_population": 61,
"gnomad_exomes_af": 0.0000383093,
"gnomad_genomes_af": 0.0000328252,
"gnomad_exomes_ac": 56,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5899999737739563,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.042,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6,BP7",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000324001.8",
"gene_symbol": "PRX",
"hgnc_id": 13797,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.237C>T",
"hgvs_p": "p.Asp79Asp"
}
],
"clinvar_disease": "Charcot-Marie-Tooth disease type 4,Charcot-Marie-Tooth disease type 4F,Inborn genetic diseases,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3",
"phenotype_combined": "not specified|Charcot-Marie-Tooth disease type 4F|Charcot-Marie-Tooth disease type 4|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}