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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: 19-18845988-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=18845988&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 18845988,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000262803.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "c.240C>T",
"hgvs_p": "p.Pro80Pro",
"transcript": "NM_002911.4",
"protein_id": "NP_002902.2",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 1118,
"cds_start": 240,
"cds_end": null,
"cds_length": 3357,
"cdna_start": 491,
"cdna_end": null,
"cdna_length": 5321,
"mane_select": "ENST00000262803.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "c.240C>T",
"hgvs_p": "p.Pro80Pro",
"transcript": "ENST00000262803.10",
"protein_id": "ENSP00000262803.5",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 1118,
"cds_start": 240,
"cds_end": null,
"cds_length": 3357,
"cdna_start": 491,
"cdna_end": null,
"cdna_length": 5321,
"mane_select": "NM_002911.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "c.240C>T",
"hgvs_p": "p.Pro80Pro",
"transcript": "ENST00000599848.5",
"protein_id": "ENSP00000470142.1",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 1129,
"cds_start": 240,
"cds_end": null,
"cds_length": 3390,
"cdna_start": 449,
"cdna_end": null,
"cdna_length": 5311,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "c.240C>T",
"hgvs_p": "p.Pro80Pro",
"transcript": "NM_001297549.2",
"protein_id": "NP_001284478.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 1129,
"cds_start": 240,
"cds_end": null,
"cds_length": 3390,
"cdna_start": 491,
"cdna_end": null,
"cdna_length": 5354,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "c.240C>T",
"hgvs_p": "p.Pro80Pro",
"transcript": "ENST00000704676.1",
"protein_id": "ENSP00000515988.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 1113,
"cds_start": 240,
"cds_end": null,
"cds_length": 3342,
"cdna_start": 491,
"cdna_end": null,
"cdna_length": 5306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "c.240C>T",
"hgvs_p": "p.Pro80Pro",
"transcript": "XM_017027105.3",
"protein_id": "XP_016882594.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 1137,
"cds_start": 240,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 491,
"cdna_end": null,
"cdna_length": 5378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "c.240C>T",
"hgvs_p": "p.Pro80Pro",
"transcript": "XM_017027106.3",
"protein_id": "XP_016882595.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 1126,
"cds_start": 240,
"cds_end": null,
"cds_length": 3381,
"cdna_start": 491,
"cdna_end": null,
"cdna_length": 5345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "c.111C>T",
"hgvs_p": "p.Pro37Pro",
"transcript": "XM_047439191.1",
"protein_id": "XP_047295147.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 1094,
"cds_start": 111,
"cds_end": null,
"cds_length": 3285,
"cdna_start": 126,
"cdna_end": null,
"cdna_length": 5013,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "n.163C>T",
"hgvs_p": null,
"transcript": "ENST00000601981.6",
"protein_id": null,
"transcript_support_level": 5,
"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": 4990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "n.240C>T",
"hgvs_p": null,
"transcript": "ENST00000704677.1",
"protein_id": "ENSP00000515989.1",
"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": 5328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"hgvs_c": "n.240C>T",
"hgvs_p": null,
"transcript": "ENST00000704678.1",
"protein_id": "ENSP00000515990.1",
"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": 2055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "UPF1",
"gene_hgnc_id": 9962,
"dbsnp": "rs35427308",
"frequency_reference_population": 0.0030484519,
"hom_count_reference_population": 12,
"allele_count_reference_population": 4920,
"gnomad_exomes_af": 0.00308764,
"gnomad_genomes_af": 0.00267239,
"gnomad_exomes_ac": 4513,
"gnomad_genomes_ac": 407,
"gnomad_exomes_homalt": 11,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5799999833106995,
"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": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.929,
"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_Strong,BP6_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000262803.10",
"gene_symbol": "UPF1",
"hgnc_id": 9962,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.240C>T",
"hgvs_p": "p.Pro80Pro"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}