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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: 16-31459780-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=31459780&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 31459780,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000268314.9",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.256C>T",
"hgvs_p": "p.Gln86*",
"transcript": "NM_001105247.2",
"protein_id": "NP_001098717.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 935,
"cds_start": 256,
"cds_end": null,
"cds_length": 2808,
"cdna_start": 280,
"cdna_end": null,
"cdna_length": 3108,
"mane_select": "ENST00000268314.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.256C>T",
"hgvs_p": "p.Gln86*",
"transcript": "ENST00000268314.9",
"protein_id": "ENSP00000268314.4",
"transcript_support_level": 5,
"aa_start": 86,
"aa_end": null,
"aa_length": 935,
"cds_start": 256,
"cds_end": null,
"cds_length": 2808,
"cdna_start": 280,
"cdna_end": null,
"cdna_length": 3108,
"mane_select": "NM_001105247.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.256C>T",
"hgvs_p": "p.Gln86*",
"transcript": "ENST00000457010.6",
"protein_id": "ENSP00000399561.2",
"transcript_support_level": 1,
"aa_start": 86,
"aa_end": null,
"aa_length": 725,
"cds_start": 256,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 4844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.541C>T",
"hgvs_p": "p.Gln181*",
"transcript": "NM_001288767.2",
"protein_id": "NP_001275696.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 1030,
"cds_start": 541,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 634,
"cdna_end": null,
"cdna_length": 3462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.541C>T",
"hgvs_p": "p.Gln181*",
"transcript": "ENST00000408912.7",
"protein_id": "ENSP00000386125.3",
"transcript_support_level": 2,
"aa_start": 181,
"aa_end": null,
"aa_length": 1030,
"cds_start": 541,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 858,
"cdna_end": null,
"cdna_length": 3626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.352C>T",
"hgvs_p": "p.Gln118*",
"transcript": "NM_001301820.1",
"protein_id": "NP_001288749.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 967,
"cds_start": 352,
"cds_end": null,
"cds_length": 2904,
"cdna_start": 800,
"cdna_end": null,
"cdna_length": 3630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.256C>T",
"hgvs_p": "p.Gln86*",
"transcript": "ENST00000563544.5",
"protein_id": "ENSP00000456877.1",
"transcript_support_level": 2,
"aa_start": 86,
"aa_end": null,
"aa_length": 935,
"cds_start": 256,
"cds_end": null,
"cds_length": 2808,
"cdna_start": 802,
"cdna_end": null,
"cdna_length": 3549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.256C>T",
"hgvs_p": "p.Gln86*",
"transcript": "NM_024742.2",
"protein_id": "NP_079018.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 725,
"cds_start": 256,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 785,
"cdna_end": null,
"cdna_length": 4673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.352C>T",
"hgvs_p": "p.Gln118*",
"transcript": "XM_006721091.4",
"protein_id": "XP_006721154.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 973,
"cds_start": 352,
"cds_end": null,
"cds_length": 2922,
"cdna_start": 800,
"cdna_end": null,
"cdna_length": 3646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.256C>T",
"hgvs_p": "p.Gln86*",
"transcript": "XM_047434651.1",
"protein_id": "XP_047290607.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 941,
"cds_start": 256,
"cds_end": null,
"cds_length": 2826,
"cdna_start": 785,
"cdna_end": null,
"cdna_length": 3631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "c.-183C>T",
"hgvs_p": null,
"transcript": "ENST00000564900.1",
"protein_id": "ENSP00000456571.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 597,
"cds_start": -4,
"cds_end": null,
"cds_length": 1794,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2072,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"hgvs_c": "n.-216C>T",
"hgvs_p": null,
"transcript": "ENST00000564514.2",
"protein_id": "ENSP00000454430.2",
"transcript_support_level": 4,
"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": 586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000260267",
"gene_hgnc_id": null,
"hgvs_c": "n.-44G>A",
"hgvs_p": null,
"transcript": "ENST00000564629.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 3026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ARMC5",
"gene_hgnc_id": 25781,
"dbsnp": "rs587777660",
"frequency_reference_population": 7.203449e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.20345e-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": 0.5299999713897705,
"computational_prediction_selected": "Pathogenic",
"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": 0.53,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.528,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000268314.9",
"gene_symbol": "ARMC5",
"hgnc_id": 25781,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD",
"hgvs_c": "c.256C>T",
"hgvs_p": "p.Gln86*"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000564629.1",
"gene_symbol": "ENSG00000260267",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-44G>A",
"hgvs_p": null
}
],
"clinvar_disease": "ACTH-independent macronodular adrenal hyperplasia 2",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "ACTH-independent macronodular adrenal hyperplasia 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}