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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: 3-46979634-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=46979634&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 46979634,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "NM_144716.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.-73+2298T>C",
"hgvs_p": null,
"transcript": "NM_144716.6",
"protein_id": "NP_653317.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": null,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_144716.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.-73+2298T>C",
"hgvs_p": null,
"transcript": "ENST00000292314.6",
"protein_id": "ENSP00000292314.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": null,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000292314.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.-215+2298T>C",
"hgvs_p": null,
"transcript": "ENST00000425441.5",
"protein_id": "ENSP00000416263.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 166,
"cds_start": null,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000425441.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.-112+2298T>C",
"hgvs_p": null,
"transcript": "ENST00000446836.5",
"protein_id": "ENSP00000387490.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 88,
"cds_start": null,
"cds_end": null,
"cds_length": 267,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000446836.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "n.79+2298T>C",
"hgvs_p": null,
"transcript": "ENST00000492819.1",
"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": "ENST00000492819.1"
},
{
"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": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "NM_015175.3",
"protein_id": "NP_055990.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2754,
"cds_start": null,
"cds_end": null,
"cds_length": 8265,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000450053.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015175.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "ENST00000450053.8",
"protein_id": "ENSP00000415034.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 2754,
"cds_start": null,
"cds_end": null,
"cds_length": 8265,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015175.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450053.8"
},
{
"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": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "ENST00000933460.1",
"protein_id": "ENSP00000603519.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2674,
"cds_start": null,
"cds_end": null,
"cds_length": 8025,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933460.1"
},
{
"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": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "ENST00000952756.1",
"protein_id": "ENSP00000622815.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2604,
"cds_start": null,
"cds_end": null,
"cds_length": 7815,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952756.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.-209T>C",
"hgvs_p": null,
"transcript": "ENST00000605875.1",
"protein_id": "ENSP00000473887.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 80,
"cds_start": null,
"cds_end": null,
"cds_length": 244,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000605875.1"
},
{
"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": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "XM_006713072.4",
"protein_id": "XP_006713135.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2727,
"cds_start": null,
"cds_end": null,
"cds_length": 8184,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006713072.4"
},
{
"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": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "XM_011533533.3",
"protein_id": "XP_011531835.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2724,
"cds_start": null,
"cds_end": null,
"cds_length": 8175,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533533.3"
},
{
"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": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "XM_047447786.1",
"protein_id": "XP_047303742.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2631,
"cds_start": null,
"cds_end": null,
"cds_length": 7896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447786.1"
},
{
"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": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "XM_047447787.1",
"protein_id": "XP_047303743.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2604,
"cds_start": null,
"cds_end": null,
"cds_length": 7815,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447787.1"
},
{
"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": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "XM_047447790.1",
"protein_id": "XP_047303746.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2435,
"cds_start": null,
"cds_end": null,
"cds_length": 7308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447790.1"
},
{
"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": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "XM_047447792.1",
"protein_id": "XP_047303748.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1793,
"cds_start": null,
"cds_end": null,
"cds_length": 5382,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447792.1"
},
{
"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": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NBEAL2",
"gene_hgnc_id": 31928,
"hgvs_c": "c.-228A>G",
"hgvs_p": null,
"transcript": "XM_047447793.1",
"protein_id": "XP_047303749.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1670,
"cds_start": null,
"cds_end": null,
"cds_length": 5013,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447793.1"
}
],
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"dbsnp": "rs13062681",
"frequency_reference_population": 0.52860177,
"hom_count_reference_population": 44634,
"allele_count_reference_population": 161454,
"gnomad_exomes_af": 0.56593,
"gnomad_genomes_af": 0.490944,
"gnomad_exomes_ac": 86808,
"gnomad_genomes_ac": 74646,
"gnomad_exomes_homalt": 24822,
"gnomad_genomes_homalt": 19812,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7200000286102295,
"computational_prediction_selected": "Benign",
"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": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.708,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_144716.6",
"gene_symbol": "CCDC12",
"hgnc_id": 28332,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-73+2298T>C",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_015175.3",
"gene_symbol": "NBEAL2",
"hgnc_id": 31928,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.-228A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}