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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: 9-131091599-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=131091599&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 131091599,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000361069.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4540C>T",
"hgvs_p": "p.Arg1514Cys",
"transcript": "NM_006059.4",
"protein_id": "NP_006050.3",
"transcript_support_level": null,
"aa_start": 1514,
"aa_end": null,
"aa_length": 1575,
"cds_start": 4540,
"cds_end": null,
"cds_length": 4728,
"cdna_start": 4581,
"cdna_end": null,
"cdna_length": 7455,
"mane_select": "ENST00000361069.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4540C>T",
"hgvs_p": "p.Arg1514Cys",
"transcript": "ENST00000361069.9",
"protein_id": "ENSP00000354360.4",
"transcript_support_level": 2,
"aa_start": 1514,
"aa_end": null,
"aa_length": 1575,
"cds_start": 4540,
"cds_end": null,
"cds_length": 4728,
"cdna_start": 4581,
"cdna_end": null,
"cdna_length": 7455,
"mane_select": "NM_006059.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.Arg195Cys",
"transcript": "ENST00000355452.5",
"protein_id": "ENSP00000347627.5",
"transcript_support_level": 1,
"aa_start": 195,
"aa_end": null,
"aa_length": 256,
"cds_start": 583,
"cds_end": null,
"cds_length": 771,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 3459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.676C>T",
"hgvs_p": "p.Arg226Cys",
"transcript": "ENST00000678758.1",
"protein_id": "ENSP00000503612.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 287,
"cds_start": 676,
"cds_end": null,
"cds_length": 864,
"cdna_start": 676,
"cdna_end": null,
"cdna_length": 3550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4558C>T",
"hgvs_p": "p.Arg1520Cys",
"transcript": "XM_011518121.2",
"protein_id": "XP_011516423.1",
"transcript_support_level": null,
"aa_start": 1520,
"aa_end": null,
"aa_length": 1581,
"cds_start": 4558,
"cds_end": null,
"cds_length": 4746,
"cdna_start": 4599,
"cdna_end": null,
"cdna_length": 7473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "n.357C>T",
"hgvs_p": null,
"transcript": "ENST00000462567.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "n.2113C>T",
"hgvs_p": null,
"transcript": "ENST00000678544.1",
"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": 2572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124902289",
"gene_hgnc_id": null,
"hgvs_c": "n.97+1677G>A",
"hgvs_p": null,
"transcript": "XR_007061825.1",
"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": 315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"dbsnp": "rs145980204",
"frequency_reference_population": 0.00006780206,
"hom_count_reference_population": 1,
"allele_count_reference_population": 108,
"gnomad_exomes_af": 0.000067336,
"gnomad_genomes_af": 0.0000722088,
"gnomad_exomes_ac": 97,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11237144470214844,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.089,
"revel_prediction": "Benign",
"alphamissense_score": 0.1382,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.714,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000361069.9",
"gene_symbol": "LAMC3",
"hgnc_id": 6494,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.4540C>T",
"hgvs_p": "p.Arg1514Cys"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007061825.1",
"gene_symbol": "LOC124902289",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.97+1677G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "not specified|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}