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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: 3-179419444-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=179419444&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 179419444,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000232564.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "NM_021629.4",
"protein_id": "NP_067642.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 340,
"cds_start": 158,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 325,
"cdna_end": null,
"cdna_length": 6315,
"mane_select": "ENST00000232564.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "ENST00000232564.8",
"protein_id": "ENSP00000232564.3",
"transcript_support_level": 1,
"aa_start": 53,
"aa_end": null,
"aa_length": 340,
"cds_start": 158,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 325,
"cdna_end": null,
"cdna_length": 6315,
"mane_select": "NM_021629.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "ENST00000466899.6",
"protein_id": "ENSP00000420066.2",
"transcript_support_level": 1,
"aa_start": 53,
"aa_end": null,
"aa_length": 242,
"cds_start": 158,
"cds_end": null,
"cds_length": 729,
"cdna_start": 158,
"cdna_end": null,
"cdna_length": 1170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "ENST00000674862.1",
"protein_id": "ENSP00000502628.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 340,
"cds_start": 158,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 308,
"cdna_end": null,
"cdna_length": 1173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "ENST00000676128.1",
"protein_id": "ENSP00000501882.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 340,
"cds_start": 158,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 422,
"cdna_end": null,
"cdna_length": 6386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.119G>A",
"hgvs_p": "p.Gly40Asp",
"transcript": "ENST00000468623.6",
"protein_id": "ENSP00000419693.2",
"transcript_support_level": 2,
"aa_start": 40,
"aa_end": null,
"aa_length": 327,
"cds_start": 119,
"cds_end": null,
"cds_length": 984,
"cdna_start": 119,
"cdna_end": null,
"cdna_length": 984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "ENST00000675901.1",
"protein_id": "ENSP00000501992.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 322,
"cds_start": 158,
"cds_end": null,
"cds_length": 969,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 1187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "ENST00000674927.1",
"protein_id": "ENSP00000501774.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 306,
"cds_start": 158,
"cds_end": null,
"cds_length": 921,
"cdna_start": 158,
"cdna_end": null,
"cdna_length": 1696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.50G>A",
"hgvs_p": "p.Gly17Asp",
"transcript": "ENST00000674713.1",
"protein_id": "ENSP00000502144.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 304,
"cds_start": 50,
"cds_end": null,
"cds_length": 915,
"cdna_start": 331,
"cdna_end": null,
"cdna_length": 1196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "ENST00000465153.2",
"protein_id": "ENSP00000502010.1",
"transcript_support_level": 3,
"aa_start": 53,
"aa_end": null,
"aa_length": 245,
"cds_start": 158,
"cds_end": null,
"cds_length": 738,
"cdna_start": 158,
"cdna_end": null,
"cdna_length": 978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "ENST00000497513.1",
"protein_id": "ENSP00000420606.1",
"transcript_support_level": 4,
"aa_start": 53,
"aa_end": null,
"aa_length": 78,
"cds_start": 158,
"cds_end": null,
"cds_length": 239,
"cdna_start": 490,
"cdna_end": null,
"cdna_length": 571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "XM_005247692.3",
"protein_id": "XP_005247749.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 340,
"cds_start": 158,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 3842,
"cdna_end": null,
"cdna_length": 9832,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "XM_006713721.3",
"protein_id": "XP_006713784.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 340,
"cds_start": 158,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 438,
"cdna_end": null,
"cdna_length": 6428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "XM_047448653.1",
"protein_id": "XP_047304609.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 340,
"cds_start": 158,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 6424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp",
"transcript": "XM_047448654.1",
"protein_id": "XP_047304610.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 340,
"cds_start": 158,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 6424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GNB4",
"gene_hgnc_id": 20731,
"dbsnp": "rs387907340",
"frequency_reference_population": 6.844871e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84487e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9401412010192871,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.862,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9999,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.3,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.776,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000232564.8",
"gene_symbol": "GNB4",
"hgnc_id": 20731,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Gly53Asp"
}
],
"clinvar_disease": "Charcot-Marie-Tooth disease dominant intermediate F",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Charcot-Marie-Tooth disease dominant intermediate F",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}