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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: 19-6467508-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=6467508&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DENND1C",
"hgnc_id": 26225,
"hgvs_c": "c.2402G>A",
"hgvs_p": "p.Gly801Asp",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_024898.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 50,
"alphamissense_prediction": null,
"alphamissense_score": 0.1509,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.51,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.06433740258216858,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 801,
"aa_ref": "G",
"aa_start": 801,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2795,
"cdna_start": 2494,
"cds_end": null,
"cds_length": 2406,
"cds_start": 2402,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "NM_024898.4",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2402G>A",
"hgvs_p": "p.Gly801Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000381480.7",
"protein_coding": true,
"protein_id": "NP_079174.2",
"strand": false,
"transcript": "NM_024898.4",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 801,
"aa_ref": "G",
"aa_start": 801,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2795,
"cdna_start": 2494,
"cds_end": null,
"cds_length": 2406,
"cds_start": 2402,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000381480.7",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2402G>A",
"hgvs_p": "p.Gly801Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024898.4",
"protein_coding": true,
"protein_id": "ENSP00000370889.1",
"strand": false,
"transcript": "ENST00000381480.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2933,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000590867.5",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "n.*1634G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000465675.1",
"strand": false,
"transcript": "ENST00000590867.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2933,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000590867.5",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "n.*1634G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000465675.1",
"strand": false,
"transcript": "ENST00000590867.5",
"transcript_support_level": 1
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 788,
"aa_ref": "G",
"aa_start": 788,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2517,
"cdna_start": 2455,
"cds_end": null,
"cds_length": 2367,
"cds_start": 2363,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000871259.1",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2363G>A",
"hgvs_p": "p.Gly788Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541318.1",
"strand": false,
"transcript": "ENST00000871259.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 759,
"aa_ref": "G",
"aa_start": 759,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2669,
"cdna_start": 2368,
"cds_end": null,
"cds_length": 2280,
"cds_start": 2276,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000871258.1",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2276G>A",
"hgvs_p": "p.Gly759Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541317.1",
"strand": false,
"transcript": "ENST00000871258.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 757,
"aa_ref": "G",
"aa_start": 757,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2686,
"cdna_start": 2385,
"cds_end": null,
"cds_length": 2274,
"cds_start": 2270,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "NM_001290331.2",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2270G>A",
"hgvs_p": "p.Gly757Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001277260.1",
"strand": false,
"transcript": "NM_001290331.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 757,
"aa_ref": "G",
"aa_start": 757,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2395,
"cdna_start": 2385,
"cds_end": null,
"cds_length": 2274,
"cds_start": 2270,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000543576.5",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2270G>A",
"hgvs_p": "p.Gly757Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000437805.1",
"strand": false,
"transcript": "ENST00000543576.5",
"transcript_support_level": 2
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 938,
"aa_ref": "G",
"aa_start": 938,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4422,
"cdna_start": 4121,
"cds_end": null,
"cds_length": 2817,
"cds_start": 2813,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_024451727.2",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2813G>A",
"hgvs_p": "p.Gly938Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024307495.1",
"strand": false,
"transcript": "XM_024451727.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 896,
"aa_ref": "G",
"aa_start": 896,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4296,
"cdna_start": 3995,
"cds_end": null,
"cds_length": 2691,
"cds_start": 2687,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_006722905.4",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2687G>A",
"hgvs_p": "p.Gly896Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006722968.3",
"strand": false,
"transcript": "XM_006722905.4",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 759,
"aa_ref": "G",
"aa_start": 759,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2669,
"cdna_start": 2368,
"cds_end": null,
"cds_length": 2280,
"cds_start": 2276,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_047439458.1",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2276G>A",
"hgvs_p": "p.Gly759Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295414.1",
"strand": false,
"transcript": "XM_047439458.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 757,
"aa_ref": "G",
"aa_start": 757,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2734,
"cdna_start": 2433,
"cds_end": null,
"cds_length": 2274,
"cds_start": 2270,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_006722906.4",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2270G>A",
"hgvs_p": "p.Gly757Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006722969.1",
"strand": false,
"transcript": "XM_006722906.4",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 757,
"aa_ref": "G",
"aa_start": 757,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2730,
"cdna_start": 2429,
"cds_end": null,
"cds_length": 2274,
"cds_start": 2270,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_011528318.3",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.2270G>A",
"hgvs_p": "p.Gly757Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011526620.1",
"strand": false,
"transcript": "XM_011528318.3",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 561,
"aa_ref": "G",
"aa_start": 561,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2148,
"cdna_start": 1847,
"cds_end": null,
"cds_length": 1686,
"cds_start": 1682,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_047439459.1",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "c.1682G>A",
"hgvs_p": "p.Gly561Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295415.1",
"strand": false,
"transcript": "XM_047439459.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2446,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000590444.5",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "n.2145G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000590444.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2422,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000590818.5",
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"hgvs_c": "n.2122G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000590818.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs745631501",
"effect": "missense_variant",
"frequency_reference_population": 0.00003147073,
"gene_hgnc_id": 26225,
"gene_symbol": "DENND1C",
"gnomad_exomes_ac": 47,
"gnomad_exomes_af": 0.0000327146,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197223,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.501,
"pos": 6467508,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.052,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_024898.4"
}
]
}