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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: 4-80202184-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=80202184&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 16,
"criteria": [
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRDM8",
"hgnc_id": 13993,
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -16,
"transcript": "NM_020226.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BS1,BS2",
"acmg_score": -16,
"allele_count_reference_population": 1507,
"alphamissense_prediction": null,
"alphamissense_score": 0.0801,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.47,
"chr": "4",
"clinvar_classification": "Benign",
"clinvar_disease": "Early-onset Lafora body disease,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.005569040775299072,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 985,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001099403.2",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000415738.3",
"protein_coding": true,
"protein_id": "NP_001092873.1",
"strand": true,
"transcript": "NM_001099403.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 985,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000415738.3",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001099403.2",
"protein_coding": true,
"protein_id": "ENSP00000406998.2",
"strand": true,
"transcript": "ENST00000415738.3",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4095,
"cdna_start": 1953,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000339711.8",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000339764.4",
"strand": true,
"transcript": "ENST00000339711.8",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 426,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2514,
"cdna_start": 1953,
"cds_end": null,
"cds_length": 1283,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000515013.5",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000425149.1",
"strand": true,
"transcript": "ENST00000515013.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 690,
"aa_ref": "P",
"aa_start": 242,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3341,
"cdna_start": 1199,
"cds_end": null,
"cds_length": 2073,
"cds_start": 725,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000952376.1",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.725C>A",
"hgvs_p": "p.Pro242Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622435.1",
"strand": true,
"transcript": "ENST00000952376.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4098,
"cdna_start": 1953,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_020226.4",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_064611.3",
"strand": true,
"transcript": "NM_020226.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3706,
"cdna_start": 1561,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000504452.5",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423985.1",
"strand": true,
"transcript": "ENST00000504452.5",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3782,
"cdna_start": 1642,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000861821.1",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531880.1",
"strand": true,
"transcript": "ENST00000861821.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2819,
"cdna_start": 926,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000861822.1",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531881.1",
"strand": true,
"transcript": "ENST00000861822.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4014,
"cdna_start": 1877,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000952373.1",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622432.1",
"strand": true,
"transcript": "ENST00000952373.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3378,
"cdna_start": 1236,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000952374.1",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622433.1",
"strand": true,
"transcript": "ENST00000952374.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3371,
"cdna_start": 1274,
"cds_end": null,
"cds_length": 2070,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000952375.1",
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"hgvs_c": "c.722C>A",
"hgvs_p": "p.Pro241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622434.1",
"strand": true,
"transcript": "ENST00000952375.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs200010979",
"effect": "missense_variant",
"frequency_reference_population": 0.00093486236,
"gene_hgnc_id": 13993,
"gene_symbol": "PRDM8",
"gnomad_exomes_ac": 800,
"gnomad_exomes_af": 0.000547797,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_ac": 707,
"gnomad_genomes_af": 0.0046634,
"gnomad_genomes_homalt": 8,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 15,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "Early-onset Lafora body disease|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.108,
"pos": 80202184,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.131,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.33000001311302185,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.33,
"transcript": "NM_020226.4"
}
]
}