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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: 22-21633216-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=21633216&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 21633216,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_152612.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"hgvs_c": "c.35C>A",
"hgvs_p": "p.Ala12Asp",
"transcript": "NM_152612.3",
"protein_id": "NP_689825.2",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 613,
"cds_start": 35,
"cds_end": null,
"cds_length": 1842,
"cdna_start": 165,
"cdna_end": null,
"cdna_length": 2231,
"mane_select": "ENST00000292779.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"hgvs_c": "c.35C>A",
"hgvs_p": "p.Ala12Asp",
"transcript": "ENST00000292779.4",
"protein_id": "ENSP00000292779.3",
"transcript_support_level": 1,
"aa_start": 12,
"aa_end": null,
"aa_length": 613,
"cds_start": 35,
"cds_end": null,
"cds_length": 1842,
"cdna_start": 165,
"cdna_end": null,
"cdna_length": 2231,
"mane_select": "NM_152612.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"hgvs_c": "c.35C>A",
"hgvs_p": "p.Ala12Asp",
"transcript": "NM_001331066.2",
"protein_id": "NP_001317995.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 526,
"cds_start": 35,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 165,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"hgvs_c": "c.35C>A",
"hgvs_p": "p.Ala12Asp",
"transcript": "ENST00000607942.5",
"protein_id": "ENSP00000476296.1",
"transcript_support_level": 2,
"aa_start": 12,
"aa_end": null,
"aa_length": 526,
"cds_start": 35,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 209,
"cdna_end": null,
"cdna_length": 1913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"hgvs_c": "c.233C>A",
"hgvs_p": "p.Ala78Asp",
"transcript": "ENST00000425975.1",
"protein_id": "ENSP00000401637.1",
"transcript_support_level": 4,
"aa_start": 78,
"aa_end": null,
"aa_length": 151,
"cds_start": 233,
"cds_end": null,
"cds_length": 458,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"hgvs_c": "c.233C>A",
"hgvs_p": "p.Ala78Asp",
"transcript": "XM_006724159.3",
"protein_id": "XP_006724222.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 679,
"cds_start": 233,
"cds_end": null,
"cds_length": 2040,
"cdna_start": 305,
"cdna_end": null,
"cdna_length": 2371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"hgvs_c": "c.233C>A",
"hgvs_p": "p.Ala78Asp",
"transcript": "XM_047441169.1",
"protein_id": "XP_047297125.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 592,
"cds_start": 233,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 305,
"cdna_end": null,
"cdna_length": 2768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"hgvs_c": "c.233C>A",
"hgvs_p": "p.Ala78Asp",
"transcript": "XM_011529985.2",
"protein_id": "XP_011528287.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 485,
"cds_start": 233,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 305,
"cdna_end": null,
"cdna_length": 1789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"hgvs_c": "c.-34+389C>A",
"hgvs_p": null,
"transcript": "XM_011529984.3",
"protein_id": "XP_011528286.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CCDC116",
"gene_hgnc_id": 26688,
"dbsnp": "rs1396457130",
"frequency_reference_population": 0.000030308971,
"hom_count_reference_population": 0,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.0000307467,
"gnomad_genomes_af": 0.0000262864,
"gnomad_exomes_ac": 43,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3046090006828308,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.151,
"revel_prediction": "Benign",
"alphamissense_score": 0.6991,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.114,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_152612.3",
"gene_symbol": "CCDC116",
"hgnc_id": 26688,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.35C>A",
"hgvs_p": "p.Ala12Asp"
}
],
"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
}