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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: 5-129095062-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=129095062&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ISOC1",
"hgnc_id": 24254,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Pro99Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_016048.2",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "LOC124901060",
"hgnc_id": null,
"hgvs_c": "n.569G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "XR_007058926.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 12,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.7629,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.18,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.6970719695091248,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 298,
"aa_ref": "P",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1942,
"cdna_start": 314,
"cds_end": null,
"cds_length": 897,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_016048.2",
"gene_hgnc_id": 24254,
"gene_symbol": "ISOC1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Pro99Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000173527.6",
"protein_coding": true,
"protein_id": "NP_057132.2",
"strand": true,
"transcript": "NM_016048.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 298,
"aa_ref": "P",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1942,
"cdna_start": 314,
"cds_end": null,
"cds_length": 897,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000173527.6",
"gene_hgnc_id": 24254,
"gene_symbol": "ISOC1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Pro99Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_016048.2",
"protein_coding": true,
"protein_id": "ENSP00000173527.5",
"strand": true,
"transcript": "ENST00000173527.6",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 278,
"aa_ref": "P",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1873,
"cdna_start": 314,
"cds_end": null,
"cds_length": 837,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000868049.1",
"gene_hgnc_id": 24254,
"gene_symbol": "ISOC1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Pro99Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538108.1",
"strand": true,
"transcript": "ENST00000868049.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 258,
"aa_ref": "P",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1822,
"cdna_start": 314,
"cds_end": null,
"cds_length": 777,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000868048.1",
"gene_hgnc_id": 24254,
"gene_symbol": "ISOC1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Pro99Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538107.1",
"strand": true,
"transcript": "ENST00000868048.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 230,
"aa_ref": "P",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1732,
"cdna_start": 308,
"cds_end": null,
"cds_length": 693,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000918282.1",
"gene_hgnc_id": 24254,
"gene_symbol": "ISOC1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Pro99Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588341.1",
"strand": true,
"transcript": "ENST00000918282.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 190,
"aa_ref": "P",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1659,
"cdna_start": 352,
"cds_end": null,
"cds_length": 573,
"cds_start": 296,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000868047.1",
"gene_hgnc_id": 24254,
"gene_symbol": "ISOC1",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Pro99Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538106.1",
"strand": true,
"transcript": "ENST00000868047.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 283,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1886,
"cdna_start": null,
"cds_end": null,
"cds_length": 852,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000954509.1",
"gene_hgnc_id": 24254,
"gene_symbol": "ISOC1",
"hgvs_c": "c.264+32C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624568.1",
"strand": true,
"transcript": "ENST00000954509.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 187,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 581,
"cdna_start": null,
"cds_end": null,
"cds_length": 565,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000514194.5",
"gene_hgnc_id": 24254,
"gene_symbol": "ISOC1",
"hgvs_c": "c.282+14C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000421273.1",
"strand": true,
"transcript": "ENST00000514194.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2705,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XR_007058926.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC124901060",
"hgvs_c": "n.569G>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": "XR_007058926.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1346218852",
"effect": "missense_variant",
"frequency_reference_population": 0.0000076004494,
"gene_hgnc_id": 24254,
"gene_symbol": "ISOC1",
"gnomad_exomes_ac": 9,
"gnomad_exomes_af": 0.00000630908,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000196931,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.714,
"pos": 129095062,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.19,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_016048.2"
}
]
}