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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: 11-124922760-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=124922760&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 124922760,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000298251.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEPACAM",
"gene_hgnc_id": 26361,
"hgvs_c": "c.862C>T",
"hgvs_p": "p.Arg288Cys",
"transcript": "NM_152722.5",
"protein_id": "NP_689935.2",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 416,
"cds_start": 862,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 3225,
"mane_select": "ENST00000298251.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEPACAM",
"gene_hgnc_id": 26361,
"hgvs_c": "c.862C>T",
"hgvs_p": "p.Arg288Cys",
"transcript": "ENST00000298251.5",
"protein_id": "ENSP00000298251.4",
"transcript_support_level": 1,
"aa_start": 288,
"aa_end": null,
"aa_length": 416,
"cds_start": 862,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 3225,
"mane_select": "NM_152722.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEPACAM",
"gene_hgnc_id": 26361,
"hgvs_c": "c.862C>T",
"hgvs_p": "p.Arg288Cys",
"transcript": "NM_001411043.1",
"protein_id": "NP_001397972.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 468,
"cds_start": 862,
"cds_end": null,
"cds_length": 1407,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 3381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEPACAM",
"gene_hgnc_id": 26361,
"hgvs_c": "c.862C>T",
"hgvs_p": "p.Arg288Cys",
"transcript": "ENST00000703807.1",
"protein_id": "ENSP00000515485.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 468,
"cds_start": 862,
"cds_end": null,
"cds_length": 1407,
"cdna_start": 898,
"cdna_end": null,
"cdna_length": 3376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEPACAM",
"gene_hgnc_id": 26361,
"hgvs_c": "c.862C>T",
"hgvs_p": "p.Arg288Cys",
"transcript": "NM_001441320.1",
"protein_id": "NP_001428249.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 415,
"cds_start": 862,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 3222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000254943",
"gene_hgnc_id": null,
"hgvs_c": "n.484-20640G>A",
"hgvs_p": null,
"transcript": "ENST00000524433.2",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000254943",
"gene_hgnc_id": null,
"hgvs_c": "n.329-20640G>A",
"hgvs_p": null,
"transcript": "ENST00000828696.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000254943",
"gene_hgnc_id": null,
"hgvs_c": "n.279-20640G>A",
"hgvs_p": null,
"transcript": "ENST00000828697.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000254943",
"gene_hgnc_id": null,
"hgvs_c": "n.361-20640G>A",
"hgvs_p": null,
"transcript": "ENST00000828698.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000254943",
"gene_hgnc_id": null,
"hgvs_c": "n.291-20640G>A",
"hgvs_p": null,
"transcript": "ENST00000828699.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000254943",
"gene_hgnc_id": null,
"hgvs_c": "n.117+5037G>A",
"hgvs_p": null,
"transcript": "ENST00000828700.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 446,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC107984406",
"gene_hgnc_id": null,
"hgvs_c": "n.335-20640G>A",
"hgvs_p": null,
"transcript": "XR_001748429.3",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HEPACAM",
"gene_hgnc_id": 26361,
"dbsnp": "rs149782549",
"frequency_reference_population": 0.00042688285,
"hom_count_reference_population": 2,
"allele_count_reference_population": 689,
"gnomad_exomes_af": 0.00041864,
"gnomad_genomes_af": 0.000506086,
"gnomad_exomes_ac": 612,
"gnomad_genomes_ac": 77,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04595664143562317,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.081,
"revel_prediction": "Benign",
"alphamissense_score": 0.1029,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.836,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000298251.5",
"gene_symbol": "HEPACAM",
"hgnc_id": 26361,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.862C>T",
"hgvs_p": "p.Arg288Cys"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000524433.2",
"gene_symbol": "ENSG00000254943",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.484-20640G>A",
"hgvs_p": null
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_001748429.3",
"gene_symbol": "LOC107984406",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.335-20640G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Megalencephalic leukoencephalopathy with subcortical cysts,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2",
"phenotype_combined": "Megalencephalic leukoencephalopathy with subcortical cysts|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}