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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: 18-2694694-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=2694694&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 2694694,
"ref": "G",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "ENST00000320876.11",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.1040+1G>A",
"hgvs_p": null,
"transcript": "NM_015295.3",
"protein_id": "NP_056110.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
"cds_end": null,
"cds_length": 6018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "ENST00000320876.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.1040+1G>A",
"hgvs_p": null,
"transcript": "ENST00000320876.11",
"protein_id": "ENSP00000326603.7",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
"cds_end": null,
"cds_length": 6018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "NM_015295.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.1040+1G>A",
"hgvs_p": null,
"transcript": "ENST00000688342.1",
"protein_id": "ENSP00000508422.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1961,
"cds_start": -4,
"cds_end": null,
"cds_length": 5886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.274+1G>A",
"hgvs_p": null,
"transcript": "ENST00000581226.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000266049",
"gene_hgnc_id": null,
"hgvs_c": "n.371-2814C>T",
"hgvs_p": null,
"transcript": "ENST00000583546.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.1197+1G>A",
"hgvs_p": null,
"transcript": "ENST00000684915.1",
"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": 3534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.318+1G>A",
"hgvs_p": null,
"transcript": "ENST00000693213.1",
"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": 6737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.1040+1G>A",
"hgvs_p": null,
"transcript": "XM_011525642.2",
"protein_id": "XP_011523944.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2067,
"cds_start": -4,
"cds_end": null,
"cds_length": 6204,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.656+1G>A",
"hgvs_p": null,
"transcript": "XM_047437427.1",
"protein_id": "XP_047293383.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1939,
"cds_start": -4,
"cds_end": null,
"cds_length": 5820,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.476+1G>A",
"hgvs_p": null,
"transcript": "XM_047437425.1",
"protein_id": "XP_047293381.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1879,
"cds_start": -4,
"cds_end": null,
"cds_length": 5640,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.1040+1G>A",
"hgvs_p": null,
"transcript": "XM_047437426.1",
"protein_id": "XP_047293382.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1827,
"cds_start": -4,
"cds_end": null,
"cds_length": 5484,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.1040+1G>A",
"hgvs_p": null,
"transcript": "XM_047437428.1",
"protein_id": "XP_047293384.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1450,
"cds_start": -4,
"cds_end": null,
"cds_length": 4353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.1040+1G>A",
"hgvs_p": null,
"transcript": "XM_047437429.1",
"protein_id": "XP_047293385.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1316,
"cds_start": -4,
"cds_end": null,
"cds_length": 3951,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4339,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.1390+1G>A",
"hgvs_p": null,
"transcript": "XR_001753172.2",
"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": 9051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.1390+1G>A",
"hgvs_p": null,
"transcript": "XR_007066135.1",
"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": 5706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.1390+1G>A",
"hgvs_p": null,
"transcript": "XR_935055.3",
"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": 5720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"dbsnp": "rs1245372794",
"frequency_reference_population": 0.0000037286998,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.0000034317,
"gnomad_genomes_af": 0.00000657307,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4000000059604645,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9359999895095825,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.897,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 1,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999985532734767,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 4,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong",
"BS2"
],
"verdict": "Pathogenic",
"transcript": "ENST00000320876.11",
"gene_symbol": "SMCHD1",
"hgnc_id": 29090,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1040+1G>A",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000583546.1",
"gene_symbol": "ENSG00000266049",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.371-2814C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Facioscapulohumeral muscular dystrophy 2,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "not provided|Facioscapulohumeral muscular dystrophy 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}