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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: 4-80202609-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=80202609&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 80202609,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_020226.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "NM_001099403.2",
"protein_id": "NP_001092873.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000415738.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001099403.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "ENST00000415738.3",
"protein_id": "ENSP00000406998.2",
"transcript_support_level": 1,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001099403.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415738.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "ENST00000339711.8",
"protein_id": "ENSP00000339764.4",
"transcript_support_level": 1,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000339711.8"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "ENST00000515013.5",
"protein_id": "ENSP00000425149.1",
"transcript_support_level": 1,
"aa_start": 383,
"aa_end": null,
"aa_length": 426,
"cds_start": 1147,
"cds_end": null,
"cds_length": 1283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515013.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1150C>T",
"hgvs_p": "p.Arg384Cys",
"transcript": "ENST00000952376.1",
"protein_id": "ENSP00000622435.1",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 690,
"cds_start": 1150,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952376.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "NM_020226.4",
"protein_id": "NP_064611.3",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020226.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "ENST00000504452.5",
"protein_id": "ENSP00000423985.1",
"transcript_support_level": 5,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000504452.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "ENST00000861821.1",
"protein_id": "ENSP00000531880.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861821.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "ENST00000861822.1",
"protein_id": "ENSP00000531881.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861822.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "ENST00000952373.1",
"protein_id": "ENSP00000622432.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952373.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "ENST00000952374.1",
"protein_id": "ENSP00000622433.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952374.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "ENST00000952375.1",
"protein_id": "ENSP00000622434.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 689,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952375.1"
}
],
"gene_symbol": "PRDM8",
"gene_hgnc_id": 13993,
"dbsnp": "rs775117967",
"frequency_reference_population": 0.0000084879775,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000797407,
"gnomad_genomes_af": 0.0000131487,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.49554142355918884,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.585,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7961,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.093,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_020226.4",
"gene_symbol": "PRDM8",
"hgnc_id": 13993,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys"
}
],
"clinvar_disease": "Early-onset Lafora body disease",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Early-onset Lafora body disease",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}