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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: 21-43774330-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=43774330&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 43774330,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_000100.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSTB",
"gene_hgnc_id": 2482,
"hgvs_c": "c.169G>A",
"hgvs_p": "p.Val57Met",
"transcript": "NM_000100.4",
"protein_id": "NP_000091.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 98,
"cds_start": 169,
"cds_end": null,
"cds_length": 297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000291568.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000100.4"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSTB",
"gene_hgnc_id": 2482,
"hgvs_c": "c.169G>A",
"hgvs_p": "p.Val57Met",
"transcript": "ENST00000291568.7",
"protein_id": "ENSP00000291568.6",
"transcript_support_level": 1,
"aa_start": 57,
"aa_end": null,
"aa_length": 98,
"cds_start": 169,
"cds_end": null,
"cds_length": 297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000100.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000291568.7"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSTB",
"gene_hgnc_id": 2482,
"hgvs_c": "c.157G>A",
"hgvs_p": "p.Val53Met",
"transcript": "ENST00000896953.1",
"protein_id": "ENSP00000567012.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 94,
"cds_start": 157,
"cds_end": null,
"cds_length": 285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896953.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSTB",
"gene_hgnc_id": 2482,
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Val47Met",
"transcript": "ENST00000937601.1",
"protein_id": "ENSP00000607660.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 88,
"cds_start": 139,
"cds_end": null,
"cds_length": 267,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937601.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSTB",
"gene_hgnc_id": 2482,
"hgvs_c": "c.34G>A",
"hgvs_p": "p.Val12Met",
"transcript": "ENST00000639959.1",
"protein_id": "ENSP00000492123.1",
"transcript_support_level": 5,
"aa_start": 12,
"aa_end": null,
"aa_length": 53,
"cds_start": 34,
"cds_end": null,
"cds_length": 162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000639959.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSTB",
"gene_hgnc_id": 2482,
"hgvs_c": "c.*244G>A",
"hgvs_p": null,
"transcript": "ENST00000640406.1",
"protein_id": "ENSP00000492672.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 83,
"cds_start": null,
"cds_end": null,
"cds_length": 252,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640406.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSTB",
"gene_hgnc_id": 2482,
"hgvs_c": "n.594G>A",
"hgvs_p": null,
"transcript": "ENST00000675996.1",
"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": "ENST00000675996.1"
}
],
"gene_symbol": "CSTB",
"gene_hgnc_id": 2482,
"dbsnp": "rs796052394",
"frequency_reference_population": 0.0000013681538,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136815,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8743231296539307,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.5519999861717224,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.208,
"revel_prediction": "Benign",
"alphamissense_score": 0.2869,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.177,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.865151757889755,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000100.4",
"gene_symbol": "CSTB",
"hgnc_id": 2482,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.169G>A",
"hgvs_p": "p.Val57Met"
}
],
"clinvar_disease": "Progressive myoclonic epilepsy,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|Progressive myoclonic epilepsy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}