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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: 3-81577972-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=81577972&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GBE1",
"hgnc_id": 4180,
"hgvs_c": "c.1571G>T",
"hgvs_p": "p.Arg524Leu",
"inheritance_mode": "AR",
"pathogenic_score": 8,
"score": 8,
"transcript": "NM_000158.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Moderate",
"acmg_score": 8,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.8753,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.51,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9238254427909851,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 702,
"aa_ref": "R",
"aa_start": 524,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2941,
"cdna_start": 1699,
"cds_end": null,
"cds_length": 2109,
"cds_start": 1571,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_000158.4",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.1571G>T",
"hgvs_p": "p.Arg524Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000429644.7",
"protein_coding": true,
"protein_id": "NP_000149.4",
"strand": false,
"transcript": "NM_000158.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 702,
"aa_ref": "R",
"aa_start": 524,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2941,
"cdna_start": 1699,
"cds_end": null,
"cds_length": 2109,
"cds_start": 1571,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000429644.7",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.1571G>T",
"hgvs_p": "p.Arg524Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000158.4",
"protein_coding": true,
"protein_id": "ENSP00000410833.2",
"strand": false,
"transcript": "ENST00000429644.7",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 700,
"aa_ref": "R",
"aa_start": 522,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3014,
"cdna_start": 1772,
"cds_end": null,
"cds_length": 2103,
"cds_start": 1565,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000895874.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.1565G>T",
"hgvs_p": "p.Arg522Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565933.1",
"strand": false,
"transcript": "ENST00000895874.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 700,
"aa_ref": "R",
"aa_start": 522,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2667,
"cdna_start": 1588,
"cds_end": null,
"cds_length": 2103,
"cds_start": 1565,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000942742.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.1565G>T",
"hgvs_p": "p.Arg522Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612801.1",
"strand": false,
"transcript": "ENST00000942742.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 669,
"aa_ref": "R",
"aa_start": 491,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2980,
"cdna_start": 1736,
"cds_end": null,
"cds_length": 2010,
"cds_start": 1472,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000942738.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.1472G>T",
"hgvs_p": "p.Arg491Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612797.1",
"strand": false,
"transcript": "ENST00000942738.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 661,
"aa_ref": "R",
"aa_start": 483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2513,
"cdna_start": 1501,
"cds_end": null,
"cds_length": 1986,
"cds_start": 1448,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000489715.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.1448G>T",
"hgvs_p": "p.Arg483Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419638.1",
"strand": false,
"transcript": "ENST00000489715.1",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 632,
"aa_ref": "R",
"aa_start": 454,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2739,
"cdna_start": 1493,
"cds_end": null,
"cds_length": 1899,
"cds_start": 1361,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000895875.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.1361G>T",
"hgvs_p": "p.Arg454Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000565934.1",
"strand": false,
"transcript": "ENST00000895875.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 619,
"aa_ref": "R",
"aa_start": 524,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2658,
"cdna_start": 1664,
"cds_end": null,
"cds_length": 1860,
"cds_start": 1571,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000942741.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.1571G>T",
"hgvs_p": "p.Arg524Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612800.1",
"strand": false,
"transcript": "ENST00000942741.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 489,
"aa_ref": "R",
"aa_start": 311,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2297,
"cdna_start": 1060,
"cds_end": null,
"cds_length": 1470,
"cds_start": 932,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000942740.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.932G>T",
"hgvs_p": "p.Arg311Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612799.1",
"strand": false,
"transcript": "ENST00000942740.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 532,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2431,
"cdna_start": null,
"cds_end": null,
"cds_length": 1599,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000942739.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "c.1108+15936G>T",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612798.1",
"strand": false,
"transcript": "ENST00000942739.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 8416,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XR_007095662.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "n.1699G>T",
"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_007095662.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 863,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000484687.1",
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"hgvs_c": "n.-29G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000484687.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs80338673",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 4180,
"gene_symbol": "GBE1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.552,
"pos": 81577972,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.948,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000158.4"
}
]
}