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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: 2-25980767-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=25980767&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 25980767,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000264712.8",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF3C",
"gene_hgnc_id": 6321,
"hgvs_c": "c.1151A>G",
"hgvs_p": "p.Gln384Arg",
"transcript": "NM_002254.8",
"protein_id": "NP_002245.4",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 793,
"cds_start": 1151,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 1731,
"cdna_end": null,
"cdna_length": 5342,
"mane_select": "ENST00000264712.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF3C",
"gene_hgnc_id": 6321,
"hgvs_c": "c.1151A>G",
"hgvs_p": "p.Gln384Arg",
"transcript": "ENST00000264712.8",
"protein_id": "ENSP00000264712.3",
"transcript_support_level": 1,
"aa_start": 384,
"aa_end": null,
"aa_length": 793,
"cds_start": 1151,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 1731,
"cdna_end": null,
"cdna_length": 5342,
"mane_select": "NM_002254.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF3C",
"gene_hgnc_id": 6321,
"hgvs_c": "n.1151A>G",
"hgvs_p": null,
"transcript": "ENST00000417737.5",
"protein_id": "ENSP00000393676.1",
"transcript_support_level": 1,
"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": 5452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF3C",
"gene_hgnc_id": 6321,
"hgvs_c": "n.1151A>G",
"hgvs_p": null,
"transcript": "ENST00000455394.5",
"protein_id": "ENSP00000410407.1",
"transcript_support_level": 1,
"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": 5462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF3C",
"gene_hgnc_id": 6321,
"hgvs_c": "c.1151A>G",
"hgvs_p": "p.Gln384Arg",
"transcript": "ENST00000405914.1",
"protein_id": "ENSP00000385030.1",
"transcript_support_level": 5,
"aa_start": 384,
"aa_end": null,
"aa_length": 793,
"cds_start": 1151,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 1724,
"cdna_end": null,
"cdna_length": 3180,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF3C",
"gene_hgnc_id": 6321,
"hgvs_c": "c.1151A>G",
"hgvs_p": "p.Gln384Arg",
"transcript": "XM_005264299.4",
"protein_id": "XP_005264356.2",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 792,
"cds_start": 1151,
"cds_end": null,
"cds_length": 2379,
"cdna_start": 1731,
"cdna_end": null,
"cdna_length": 5339,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIF3C",
"gene_hgnc_id": 6321,
"hgvs_c": "n.-145A>G",
"hgvs_p": null,
"transcript": "ENST00000475453.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KIF3C",
"gene_hgnc_id": 6321,
"dbsnp": "rs373047696",
"frequency_reference_population": 0.000014249109,
"hom_count_reference_population": 1,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.0000102607,
"gnomad_genomes_af": 0.0000525458,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6389768123626709,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.311,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2322,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.017,
"phylop100way_prediction": "Pathogenic",
"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": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000264712.8",
"gene_symbol": "KIF3C",
"hgnc_id": 6321,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1151A>G",
"hgvs_p": "p.Gln384Arg"
}
],
"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
}