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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: 12-112167391-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=112167391&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 112167391,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001109662.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 72,
"exon_rank_end": null,
"exon_count": 76,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HECTD4",
"gene_hgnc_id": 26611,
"hgvs_c": "c.12460G>A",
"hgvs_p": "p.Glu4154Lys",
"transcript": "NM_001388303.1",
"protein_id": "NP_001375232.1",
"transcript_support_level": null,
"aa_start": 4154,
"aa_end": null,
"aa_length": 4418,
"cds_start": 12460,
"cds_end": null,
"cds_length": 13257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000682272.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001388303.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 72,
"exon_rank_end": null,
"exon_count": 76,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HECTD4",
"gene_hgnc_id": 26611,
"hgvs_c": "c.12460G>A",
"hgvs_p": "p.Glu4154Lys",
"transcript": "ENST00000682272.1",
"protein_id": "ENSP00000507687.1",
"transcript_support_level": null,
"aa_start": 4154,
"aa_end": null,
"aa_length": 4418,
"cds_start": 12460,
"cds_end": null,
"cds_length": 13257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001388303.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682272.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 72,
"exon_rank_end": null,
"exon_count": 76,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HECTD4",
"gene_hgnc_id": 26611,
"hgvs_c": "c.12490G>A",
"hgvs_p": "p.Glu4164Lys",
"transcript": "NM_001109662.4",
"protein_id": "NP_001103132.4",
"transcript_support_level": null,
"aa_start": 4164,
"aa_end": null,
"aa_length": 4428,
"cds_start": 12490,
"cds_end": null,
"cds_length": 13287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001109662.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 72,
"exon_rank_end": null,
"exon_count": 76,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HECTD4",
"gene_hgnc_id": 26611,
"hgvs_c": "c.12454G>A",
"hgvs_p": "p.Glu4152Lys",
"transcript": "ENST00000377560.9",
"protein_id": "ENSP00000366783.7",
"transcript_support_level": 5,
"aa_start": 4152,
"aa_end": null,
"aa_length": 4416,
"cds_start": 12454,
"cds_end": null,
"cds_length": 13251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000377560.9"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 72,
"exon_rank_end": null,
"exon_count": 76,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HECTD4",
"gene_hgnc_id": 26611,
"hgvs_c": "c.12058G>A",
"hgvs_p": "p.Glu4020Lys",
"transcript": "ENST00000550722.5",
"protein_id": "ENSP00000449784.2",
"transcript_support_level": 5,
"aa_start": 4020,
"aa_end": null,
"aa_length": 4284,
"cds_start": 12058,
"cds_end": null,
"cds_length": 12855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000550722.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HECTD4",
"gene_hgnc_id": 26611,
"hgvs_c": "n.935G>A",
"hgvs_p": null,
"transcript": "ENST00000547085.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000547085.1"
},
{
"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": "HECTD4",
"gene_hgnc_id": 26611,
"hgvs_c": "n.216G>A",
"hgvs_p": null,
"transcript": "ENST00000548140.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000548140.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HECTD4",
"gene_hgnc_id": 26611,
"hgvs_c": "n.*259G>A",
"hgvs_p": null,
"transcript": "ENST00000651701.1",
"protein_id": "ENSP00000498892.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000651701.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HECTD4",
"gene_hgnc_id": 26611,
"hgvs_c": "n.*259G>A",
"hgvs_p": null,
"transcript": "ENST00000651701.1",
"protein_id": "ENSP00000498892.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000651701.1"
}
],
"gene_symbol": "HECTD4",
"gene_hgnc_id": 26611,
"dbsnp": "rs371935875",
"frequency_reference_population": 0.00007870161,
"hom_count_reference_population": 0,
"allele_count_reference_population": 127,
"gnomad_exomes_af": 0.0000807407,
"gnomad_genomes_af": 0.0000591242,
"gnomad_exomes_ac": 118,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2364911139011383,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.185,
"revel_prediction": "Benign",
"alphamissense_score": 0.1685,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.565,
"phylop100way_prediction": "Uncertain_significance",
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "NM_001109662.4",
"gene_symbol": "HECTD4",
"hgnc_id": 26611,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.12490G>A",
"hgvs_p": "p.Glu4164Lys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}