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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: 3-53872524-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=53872524&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 53872524,
"ref": "C",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_022899.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.1162G>T",
"hgvs_p": "p.Ala388Ser",
"transcript": "NM_022899.5",
"protein_id": "NP_075050.3",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 624,
"cds_start": 1162,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000335754.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022899.5"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.1162G>T",
"hgvs_p": "p.Ala388Ser",
"transcript": "ENST00000335754.8",
"protein_id": "ENSP00000336842.3",
"transcript_support_level": 2,
"aa_start": 388,
"aa_end": null,
"aa_length": 624,
"cds_start": 1162,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_022899.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335754.8"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.1162G>T",
"hgvs_p": "p.Ala388Ser",
"transcript": "ENST00000888053.1",
"protein_id": "ENSP00000558112.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 673,
"cds_start": 1162,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888053.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.1162G>T",
"hgvs_p": "p.Ala388Ser",
"transcript": "ENST00000963856.1",
"protein_id": "ENSP00000633915.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 624,
"cds_start": 1162,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963856.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.1051G>T",
"hgvs_p": "p.Ala351Ser",
"transcript": "ENST00000888052.1",
"protein_id": "ENSP00000558111.1",
"transcript_support_level": null,
"aa_start": 351,
"aa_end": null,
"aa_length": 587,
"cds_start": 1051,
"cds_end": null,
"cds_length": 1764,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888052.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.829G>T",
"hgvs_p": "p.Ala277Ser",
"transcript": "NM_001410774.1",
"protein_id": "NP_001397703.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 513,
"cds_start": 829,
"cds_end": null,
"cds_length": 1542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410774.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.829G>T",
"hgvs_p": "p.Ala277Ser",
"transcript": "ENST00000482349.5",
"protein_id": "ENSP00000419429.1",
"transcript_support_level": 2,
"aa_start": 277,
"aa_end": null,
"aa_length": 513,
"cds_start": 829,
"cds_end": null,
"cds_length": 1542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000482349.5"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.421G>T",
"hgvs_p": "p.Ala141Ser",
"transcript": "ENST00000486794.1",
"protein_id": "ENSP00000417230.1",
"transcript_support_level": 2,
"aa_start": 141,
"aa_end": null,
"aa_length": 377,
"cds_start": 421,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000486794.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.1162G>T",
"hgvs_p": "p.Ala388Ser",
"transcript": "XM_005265587.6",
"protein_id": "XP_005265644.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 624,
"cds_start": 1162,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265587.6"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "c.436G>T",
"hgvs_p": "p.Ala146Ser",
"transcript": "XM_047449238.1",
"protein_id": "XP_047305194.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 382,
"cds_start": 436,
"cds_end": null,
"cds_length": 1149,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449238.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"hgvs_c": "n.38G>T",
"hgvs_p": null,
"transcript": "ENST00000495993.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000495993.1"
}
],
"gene_symbol": "ACTR8",
"gene_hgnc_id": 14672,
"dbsnp": "rs201796393",
"frequency_reference_population": 0.00009047772,
"hom_count_reference_population": 0,
"allele_count_reference_population": 144,
"gnomad_exomes_af": 0.0000875353,
"gnomad_genomes_af": 0.000118318,
"gnomad_exomes_ac": 126,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7836564779281616,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9760000109672546,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.806,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3314,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.526,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.04,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.999833578644653,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_022899.5",
"gene_symbol": "ACTR8",
"hgnc_id": 14672,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1162G>T",
"hgvs_p": "p.Ala388Ser"
}
],
"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
}