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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: 4-10525844-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=10525844&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 10525844,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_052964.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLNK",
"gene_hgnc_id": 17438,
"hgvs_c": "c.728G>T",
"hgvs_p": "p.Ser243Ile",
"transcript": "NM_052964.4",
"protein_id": "NP_443196.2",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 428,
"cds_start": 728,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000226951.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_052964.4"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLNK",
"gene_hgnc_id": 17438,
"hgvs_c": "c.728G>T",
"hgvs_p": "p.Ser243Ile",
"transcript": "ENST00000226951.11",
"protein_id": "ENSP00000226951.6",
"transcript_support_level": 1,
"aa_start": 243,
"aa_end": null,
"aa_length": 428,
"cds_start": 728,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_052964.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000226951.11"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLNK",
"gene_hgnc_id": 17438,
"hgvs_c": "c.773G>T",
"hgvs_p": "p.Ser258Ile",
"transcript": "XM_011513775.3",
"protein_id": "XP_011512077.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 443,
"cds_start": 773,
"cds_end": null,
"cds_length": 1332,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513775.3"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLNK",
"gene_hgnc_id": 17438,
"hgvs_c": "c.773G>T",
"hgvs_p": "p.Ser258Ile",
"transcript": "XM_017007684.2",
"protein_id": "XP_016863173.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 402,
"cds_start": 773,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007684.2"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000287154",
"gene_hgnc_id": 58732,
"hgvs_c": "n.97-4290C>A",
"hgvs_p": null,
"transcript": "ENST00000663264.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000663264.1"
},
{
"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": "LOC105374482",
"gene_hgnc_id": null,
"hgvs_c": "n.262-4286C>A",
"hgvs_p": null,
"transcript": "XR_925387.4",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_925387.4"
}
],
"gene_symbol": "CLNK",
"gene_hgnc_id": 17438,
"dbsnp": "rs183771991",
"frequency_reference_population": 0.00060337456,
"hom_count_reference_population": 1,
"allele_count_reference_population": 950,
"gnomad_exomes_af": 0.000642664,
"gnomad_genomes_af": 0.000236416,
"gnomad_exomes_ac": 914,
"gnomad_genomes_ac": 36,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006952852010726929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.084,
"revel_prediction": "Benign",
"alphamissense_score": 0.1312,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.532,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_052964.4",
"gene_symbol": "CLNK",
"hgnc_id": 17438,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.728G>T",
"hgvs_p": "p.Ser243Ile"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000663264.1",
"gene_symbol": "ENSG00000287154",
"hgnc_id": 58732,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.97-4290C>A",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "XR_925387.4",
"gene_symbol": "LOC105374482",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.262-4286C>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}