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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: 7-27143364-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=27143364&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": "HOXA5",
"hgnc_id": 5106,
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Ala82Thr",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_019102.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "HOXA3",
"hgnc_id": 5104,
"hgvs_c": "c.-493-3178G>A",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_153631.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "HOXA-AS3",
"hgnc_id": 43748,
"hgvs_c": "n.173-8211C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000518848.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000273433",
"hgnc_id": null,
"hgvs_c": "n.275-3178G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000467897.2",
"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": 0.0694,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"chr": "7",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.18620029091835022,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 270,
"aa_ref": "A",
"aa_start": 82,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1670,
"cdna_start": 318,
"cds_end": null,
"cds_length": 813,
"cds_start": 244,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_019102.4",
"gene_hgnc_id": 5106,
"gene_symbol": "HOXA5",
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Ala82Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000222726.4",
"protein_coding": true,
"protein_id": "NP_061975.2",
"strand": false,
"transcript": "NM_019102.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 270,
"aa_ref": "A",
"aa_start": 82,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1670,
"cdna_start": 318,
"cds_end": null,
"cds_length": 813,
"cds_start": 244,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000222726.4",
"gene_hgnc_id": 5106,
"gene_symbol": "HOXA5",
"hgvs_c": "c.244G>A",
"hgvs_p": "p.Ala82Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_019102.4",
"protein_coding": true,
"protein_id": "ENSP00000222726.3",
"strand": false,
"transcript": "ENST00000222726.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 443,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3026,
"cdna_start": null,
"cds_end": null,
"cds_length": 1332,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_153631.3",
"gene_hgnc_id": 5104,
"gene_symbol": "HOXA3",
"hgvs_c": "c.-493-3178G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000612286.5",
"protein_coding": true,
"protein_id": "NP_705895.1",
"strand": false,
"transcript": "NM_153631.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 443,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3026,
"cdna_start": null,
"cds_end": null,
"cds_length": 1332,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000612286.5",
"gene_hgnc_id": 5104,
"gene_symbol": "HOXA3",
"hgvs_c": "c.-493-3178G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_153631.3",
"protein_coding": true,
"protein_id": "ENSP00000484411.1",
"strand": false,
"transcript": "ENST00000612286.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 443,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3142,
"cdna_start": null,
"cds_end": null,
"cds_length": 1332,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001384335.1",
"gene_hgnc_id": 5104,
"gene_symbol": "HOXA3",
"hgvs_c": "c.-609-3178G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001371264.1",
"strand": false,
"transcript": "NM_001384335.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 443,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3188,
"cdna_start": null,
"cds_end": null,
"cds_length": 1332,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001384336.1",
"gene_hgnc_id": 5104,
"gene_symbol": "HOXA3",
"hgvs_c": "c.-308-3178G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001371265.1",
"strand": false,
"transcript": "NM_001384336.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 443,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2868,
"cdna_start": null,
"cds_end": null,
"cds_length": 1332,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000851228.1",
"gene_hgnc_id": 5104,
"gene_symbol": "HOXA3",
"hgvs_c": "c.-308-3178G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521287.1",
"strand": false,
"transcript": "ENST00000851228.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 443,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2861,
"cdna_start": null,
"cds_end": null,
"cds_length": 1332,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000851229.1",
"gene_hgnc_id": 5104,
"gene_symbol": "HOXA3",
"hgvs_c": "c.-609-3178G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521288.1",
"strand": false,
"transcript": "ENST00000851229.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 443,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2887,
"cdna_start": null,
"cds_end": null,
"cds_length": 1332,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000956341.1",
"gene_hgnc_id": 5104,
"gene_symbol": "HOXA3",
"hgvs_c": "c.-308-3178G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626400.1",
"strand": false,
"transcript": "ENST00000956341.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 919,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000467897.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000273433",
"hgvs_c": "n.275-3178G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000467897.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 562,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000518848.5",
"gene_hgnc_id": 43748,
"gene_symbol": "HOXA-AS3",
"hgvs_c": "n.173-8211C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000518848.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 687,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000521197.5",
"gene_hgnc_id": 43748,
"gene_symbol": "HOXA-AS3",
"hgvs_c": "n.176+2825C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000521197.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3918,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_038832.1",
"gene_hgnc_id": 43748,
"gene_symbol": "HOXA-AS3",
"hgvs_c": "n.176+2825C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_038832.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs776598451",
"effect": "missense_variant",
"frequency_reference_population": 0.0000027949511,
"gene_hgnc_id": 5106,
"gene_symbol": "HOXA5",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000279495,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.297,
"pos": 27143364,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.225,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05000000074505806,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.05,
"transcript": "NM_019102.4"
}
]
}