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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: 6-122809291-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=122809291&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 122809291,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000368440.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.1245C>T",
"hgvs_p": "p.Asp415Asp",
"transcript": "NM_006714.5",
"protein_id": "NP_006705.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 453,
"cds_start": 1245,
"cds_end": null,
"cds_length": 1362,
"cdna_start": 1334,
"cdna_end": null,
"cdna_length": 1763,
"mane_select": "ENST00000368440.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.1245C>T",
"hgvs_p": "p.Asp415Asp",
"transcript": "ENST00000368440.5",
"protein_id": "ENSP00000357425.4",
"transcript_support_level": 1,
"aa_start": 415,
"aa_end": null,
"aa_length": 453,
"cds_start": 1245,
"cds_end": null,
"cds_length": 1362,
"cdna_start": 1334,
"cdna_end": null,
"cdna_length": 1763,
"mane_select": "NM_006714.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.852C>T",
"hgvs_p": "p.Asp284Asp",
"transcript": "NM_001286138.2",
"protein_id": "NP_001273067.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 322,
"cds_start": 852,
"cds_end": null,
"cds_length": 969,
"cdna_start": 1120,
"cdna_end": null,
"cdna_length": 1549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.852C>T",
"hgvs_p": "p.Asp284Asp",
"transcript": "ENST00000539041.5",
"protein_id": "ENSP00000442152.1",
"transcript_support_level": 2,
"aa_start": 284,
"aa_end": null,
"aa_length": 322,
"cds_start": 852,
"cds_end": null,
"cds_length": 969,
"cdna_start": 1329,
"cdna_end": null,
"cdna_length": 1755,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294893",
"gene_hgnc_id": null,
"hgvs_c": "n.330+23803G>A",
"hgvs_p": null,
"transcript": "ENST00000726593.1",
"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": 812,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294893",
"gene_hgnc_id": null,
"hgvs_c": "n.314+5012G>A",
"hgvs_p": null,
"transcript": "ENST00000726594.1",
"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": 677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"dbsnp": "rs41292584",
"frequency_reference_population": 0.057790227,
"hom_count_reference_population": 3292,
"allele_count_reference_population": 93225,
"gnomad_exomes_af": 0.0590823,
"gnomad_genomes_af": 0.0453889,
"gnomad_exomes_ac": 86316,
"gnomad_genomes_ac": 6909,
"gnomad_exomes_homalt": 3063,
"gnomad_genomes_homalt": 229,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.36000001430511475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.378,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP7,BA1",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000368440.5",
"gene_symbol": "SMPDL3A",
"hgnc_id": 17389,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1245C>T",
"hgvs_p": "p.Asp415Asp"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000726593.1",
"gene_symbol": "ENSG00000294893",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.330+23803G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}