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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: 9-131069730-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=131069730&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"BP6"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "LAMC3",
"hgnc_id": 6494,
"hgvs_c": "c.2949C>T",
"hgvs_p": "p.Cys983Cys",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -1,
"transcript": "NM_006059.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6",
"acmg_score": -1,
"allele_count_reference_population": 297,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.61,
"chr": "9",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6100000143051147,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1575,
"aa_ref": "C",
"aa_start": 983,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7455,
"cdna_start": 2990,
"cds_end": null,
"cds_length": 4728,
"cds_start": 2949,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_006059.4",
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"hgvs_c": "c.2949C>T",
"hgvs_p": "p.Cys983Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000361069.9",
"protein_coding": true,
"protein_id": "NP_006050.3",
"strand": true,
"transcript": "NM_006059.4",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1575,
"aa_ref": "C",
"aa_start": 983,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7455,
"cdna_start": 2990,
"cds_end": null,
"cds_length": 4728,
"cds_start": 2949,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000361069.9",
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"hgvs_c": "c.2949C>T",
"hgvs_p": "p.Cys983Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006059.4",
"protein_coding": true,
"protein_id": "ENSP00000354360.4",
"strand": true,
"transcript": "ENST00000361069.9",
"transcript_support_level": 2
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1581,
"aa_ref": "C",
"aa_start": 983,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5082,
"cdna_start": 2980,
"cds_end": null,
"cds_length": 4746,
"cds_start": 2949,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000868026.1",
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"hgvs_c": "c.2949C>T",
"hgvs_p": "p.Cys983Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538085.1",
"strand": true,
"transcript": "ENST00000868026.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1573,
"aa_ref": "C",
"aa_start": 983,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5018,
"cdna_start": 2978,
"cds_end": null,
"cds_length": 4722,
"cds_start": 2949,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000955224.1",
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"hgvs_c": "c.2949C>T",
"hgvs_p": "p.Cys983Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625283.1",
"strand": true,
"transcript": "ENST00000955224.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1567,
"aa_ref": "C",
"aa_start": 983,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4997,
"cdna_start": 2975,
"cds_end": null,
"cds_length": 4704,
"cds_start": 2949,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000955225.1",
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"hgvs_c": "c.2949C>T",
"hgvs_p": "p.Cys983Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625284.1",
"strand": true,
"transcript": "ENST00000955225.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1542,
"aa_ref": "C",
"aa_start": 950,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4968,
"cdna_start": 2916,
"cds_end": null,
"cds_length": 4629,
"cds_start": 2850,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000955223.1",
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"hgvs_c": "c.2850C>T",
"hgvs_p": "p.Cys950Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625282.1",
"strand": true,
"transcript": "ENST00000955223.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1472,
"aa_ref": "C",
"aa_start": 880,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4708,
"cdna_start": 2659,
"cds_end": null,
"cds_length": 4419,
"cds_start": 2640,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000940484.1",
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"hgvs_c": "c.2640C>T",
"hgvs_p": "p.Cys880Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610543.1",
"strand": true,
"transcript": "ENST00000940484.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1581,
"aa_ref": "C",
"aa_start": 983,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7473,
"cdna_start": 2990,
"cds_end": null,
"cds_length": 4746,
"cds_start": 2949,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_011518121.2",
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"hgvs_c": "c.2949C>T",
"hgvs_p": "p.Cys983Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011516423.1",
"strand": true,
"transcript": "XM_011518121.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1259,
"aa_ref": "C",
"aa_start": 983,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3995,
"cdna_start": 2990,
"cds_end": null,
"cds_length": 3780,
"cds_start": 2949,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_006716921.3",
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"hgvs_c": "c.2949C>T",
"hgvs_p": "p.Cys983Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006716984.1",
"strand": true,
"transcript": "XM_006716921.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs373660982",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00018538053,
"gene_hgnc_id": 6494,
"gene_symbol": "LAMC3",
"gnomad_exomes_ac": 286,
"gnomad_exomes_af": 0.00019725,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 11,
"gnomad_genomes_af": 0.0000722866,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.361,
"pos": 131069730,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.3400000035762787,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.34,
"transcript": "NM_006059.4"
}
]
}