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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: 10-16915037-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=16915037&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CUBN",
"hgnc_id": 2548,
"hgvs_c": "c.7346T>C",
"hgvs_p": "p.Met2449Thr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_001081.4",
"verdict": "Benign"
},
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000296126",
"hgnc_id": null,
"hgvs_c": "n.435-201A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -20,
"transcript": "ENST00000736661.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 5149,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0642,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.66,
"chr": "10",
"clinvar_classification": "Benign",
"clinvar_disease": "CUBN-related disorder,Imerslund-Grasbeck syndrome,Imerslund-Grasbeck syndrome type 1,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0033961832523345947,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3623,
"aa_ref": "M",
"aa_start": 2449,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11927,
"cdna_start": 7392,
"cds_end": null,
"cds_length": 10872,
"cds_start": 7346,
"consequences": [
"missense_variant"
],
"exon_count": 67,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "NM_001081.4",
"gene_hgnc_id": 2548,
"gene_symbol": "CUBN",
"hgvs_c": "c.7346T>C",
"hgvs_p": "p.Met2449Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000377833.10",
"protein_coding": true,
"protein_id": "NP_001072.2",
"strand": false,
"transcript": "NM_001081.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 3623,
"aa_ref": "M",
"aa_start": 2449,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 11927,
"cdna_start": 7392,
"cds_end": null,
"cds_length": 10872,
"cds_start": 7346,
"consequences": [
"missense_variant"
],
"exon_count": 67,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000377833.10",
"gene_hgnc_id": 2548,
"gene_symbol": "CUBN",
"hgvs_c": "c.7346T>C",
"hgvs_p": "p.Met2449Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001081.4",
"protein_coding": true,
"protein_id": "ENSP00000367064.4",
"strand": false,
"transcript": "ENST00000377833.10",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2867,
"aa_ref": "M",
"aa_start": 2449,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8890,
"cdna_start": 7392,
"cds_end": null,
"cds_length": 8604,
"cds_start": 7346,
"consequences": [
"missense_variant"
],
"exon_count": 55,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "XM_011519708.3",
"gene_hgnc_id": 2548,
"gene_symbol": "CUBN",
"hgvs_c": "c.7346T>C",
"hgvs_p": "p.Met2449Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011518010.1",
"strand": false,
"transcript": "XM_011519708.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2285,
"aa_ref": "M",
"aa_start": 1111,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7953,
"cdna_start": 3418,
"cds_end": null,
"cds_length": 6858,
"cds_start": 3332,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_011519709.3",
"gene_hgnc_id": 2548,
"gene_symbol": "CUBN",
"hgvs_c": "c.3332T>C",
"hgvs_p": "p.Met1111Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011518011.1",
"strand": false,
"transcript": "XM_011519709.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2277,
"aa_ref": "M",
"aa_start": 1103,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7932,
"cdna_start": 3397,
"cds_end": null,
"cds_length": 6834,
"cds_start": 3308,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_011519710.3",
"gene_hgnc_id": 2548,
"gene_symbol": "CUBN",
"hgvs_c": "c.3308T>C",
"hgvs_p": "p.Met1103Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011518012.1",
"strand": false,
"transcript": "XM_011519710.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2237,
"aa_ref": "M",
"aa_start": 1063,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7911,
"cdna_start": 3376,
"cds_end": null,
"cds_length": 6714,
"cds_start": 3188,
"consequences": [
"missense_variant"
],
"exon_count": 40,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_011519711.4",
"gene_hgnc_id": 2548,
"gene_symbol": "CUBN",
"hgvs_c": "c.3188T>C",
"hgvs_p": "p.Met1063Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011518013.1",
"strand": false,
"transcript": "XM_011519711.4",
"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": 1296,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000736661.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000296126",
"hgvs_c": "n.435-201A>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000736661.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs41301097",
"effect": "missense_variant",
"frequency_reference_population": 0.0031905547,
"gene_hgnc_id": 2548,
"gene_symbol": "CUBN",
"gnomad_exomes_ac": 4833,
"gnomad_exomes_af": 0.00330689,
"gnomad_exomes_homalt": 40,
"gnomad_genomes_ac": 316,
"gnomad_genomes_af": 0.00207439,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 40,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "Imerslund-Grasbeck syndrome|Imerslund-Grasbeck syndrome type 1|not provided|CUBN-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.385,
"pos": 16915037,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.058,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001081.4"
}
]
}