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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: 1-114587851-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=114587851&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DENND2C",
"hgnc_id": 24748,
"hgvs_c": "c.2533C>A",
"hgvs_p": "p.Arg845Ser",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_001256404.2",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"downstream_gene_variant"
],
"gene_symbol": "LOC105378914",
"hgnc_id": null,
"hgvs_c": "n.*232G>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 3,
"score": 3,
"transcript": "XR_947719.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.8452,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.06,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.7913506031036377,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 928,
"aa_ref": "R",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6177,
"cdna_start": 3173,
"cds_end": null,
"cds_length": 2787,
"cds_start": 2533,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_001256404.2",
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"hgvs_c": "c.2533C>A",
"hgvs_p": "p.Arg845Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000393274.6",
"protein_coding": true,
"protein_id": "NP_001243333.1",
"strand": false,
"transcript": "NM_001256404.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 928,
"aa_ref": "R",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6177,
"cdna_start": 3173,
"cds_end": null,
"cds_length": 2787,
"cds_start": 2533,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000393274.6",
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"hgvs_c": "c.2533C>A",
"hgvs_p": "p.Arg845Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001256404.2",
"protein_coding": true,
"protein_id": "ENSP00000376955.1",
"strand": false,
"transcript": "ENST00000393274.6",
"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": 2990,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000481894.1",
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"hgvs_c": "n.2117C>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": "ENST00000481894.1",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 928,
"aa_ref": "R",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4466,
"cdna_start": 2868,
"cds_end": null,
"cds_length": 2787,
"cds_start": 2533,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000935533.1",
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"hgvs_c": "c.2533C>A",
"hgvs_p": "p.Arg845Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000605592.1",
"strand": false,
"transcript": "ENST00000935533.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 928,
"aa_ref": "R",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5922,
"cdna_start": 2921,
"cds_end": null,
"cds_length": 2787,
"cds_start": 2533,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000970986.1",
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"hgvs_c": "c.2533C>A",
"hgvs_p": "p.Arg845Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641045.1",
"strand": false,
"transcript": "ENST00000970986.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 928,
"aa_ref": "R",
"aa_start": 845,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4806,
"cdna_start": 3206,
"cds_end": null,
"cds_length": 2787,
"cds_start": 2533,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000970987.1",
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"hgvs_c": "c.2533C>A",
"hgvs_p": "p.Arg845Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641046.1",
"strand": false,
"transcript": "ENST00000970987.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 871,
"aa_ref": "R",
"aa_start": 788,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5637,
"cdna_start": 2633,
"cds_end": null,
"cds_length": 2616,
"cds_start": 2362,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_198459.4",
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"hgvs_c": "c.2362C>A",
"hgvs_p": "p.Arg788Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_940861.3",
"strand": false,
"transcript": "NM_198459.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 871,
"aa_ref": "R",
"aa_start": 788,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5701,
"cdna_start": 2695,
"cds_end": null,
"cds_length": 2616,
"cds_start": 2362,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000393276.7",
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"hgvs_c": "c.2362C>A",
"hgvs_p": "p.Arg788Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000376957.3",
"strand": false,
"transcript": "ENST00000393276.7",
"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": 2214,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000495031.5",
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"hgvs_c": "n.140C>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": "ENST00000495031.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1531,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_947719.4",
"gene_hgnc_id": null,
"gene_symbol": "LOC105378914",
"hgvs_c": "n.*232G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_947719.4",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs748828925",
"effect": "missense_variant",
"frequency_reference_population": 6.8405444e-7,
"gene_hgnc_id": 24748,
"gene_symbol": "DENND2C",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84054e-7,
"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": "Uncertain_significance",
"phylop100way_score": 5.165,
"pos": 114587851,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.332,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001256404.2"
}
]
}