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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: 16-84889253-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=84889253&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "CRISPLD2",
"hgnc_id": 25248,
"hgvs_c": "c.1329C>T",
"hgvs_p": "p.Ala443Ala",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_031476.4",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000279622",
"hgnc_id": null,
"hgvs_c": "n.222-887G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000741212.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_score": -13,
"allele_count_reference_population": 894362,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.57,
"chr": "16",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5699999928474426,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 497,
"aa_ref": "A",
"aa_start": 443,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4583,
"cdna_start": 1552,
"cds_end": null,
"cds_length": 1494,
"cds_start": 1329,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_031476.4",
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"hgvs_c": "c.1329C>T",
"hgvs_p": "p.Ala443Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000262424.10",
"protein_coding": true,
"protein_id": "NP_113664.1",
"strand": true,
"transcript": "NM_031476.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 497,
"aa_ref": "A",
"aa_start": 443,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4583,
"cdna_start": 1552,
"cds_end": null,
"cds_length": 1494,
"cds_start": 1329,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000262424.10",
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"hgvs_c": "c.1329C>T",
"hgvs_p": "p.Ala443Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_031476.4",
"protein_coding": true,
"protein_id": "ENSP00000262424.5",
"strand": true,
"transcript": "ENST00000262424.10",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 497,
"aa_ref": "A",
"aa_start": 443,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4599,
"cdna_start": 1588,
"cds_end": null,
"cds_length": 1494,
"cds_start": 1329,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000941702.1",
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"hgvs_c": "c.1329C>T",
"hgvs_p": "p.Ala443Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611761.1",
"strand": true,
"transcript": "ENST00000941702.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 497,
"aa_ref": "A",
"aa_start": 443,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1820,
"cdna_start": 1541,
"cds_end": null,
"cds_length": 1494,
"cds_start": 1329,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000941703.1",
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"hgvs_c": "c.1329C>T",
"hgvs_p": "p.Ala443Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611762.1",
"strand": true,
"transcript": "ENST00000941703.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 496,
"aa_ref": "A",
"aa_start": 442,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2178,
"cdna_start": 1543,
"cds_end": null,
"cds_length": 1491,
"cds_start": 1326,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000567845.5",
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"hgvs_c": "c.1326C>T",
"hgvs_p": "p.Ala442Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000457183.1",
"strand": true,
"transcript": "ENST00000567845.5",
"transcript_support_level": 5
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 486,
"aa_ref": "A",
"aa_start": 432,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4554,
"cdna_start": 1523,
"cds_end": null,
"cds_length": 1461,
"cds_start": 1296,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000904767.1",
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"hgvs_c": "c.1296C>T",
"hgvs_p": "p.Ala432Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574826.1",
"strand": true,
"transcript": "ENST00000904767.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 413,
"aa_ref": "A",
"aa_start": 359,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2898,
"cdna_start": 1300,
"cds_end": null,
"cds_length": 1242,
"cds_start": 1077,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000941701.1",
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"hgvs_c": "c.1077C>T",
"hgvs_p": "p.Ala359Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611760.1",
"strand": true,
"transcript": "ENST00000941701.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 497,
"aa_ref": "A",
"aa_start": 443,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4842,
"cdna_start": 1811,
"cds_end": null,
"cds_length": 1494,
"cds_start": 1329,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_005256190.2",
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"hgvs_c": "c.1329C>T",
"hgvs_p": "p.Ala443Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005256247.1",
"strand": true,
"transcript": "XM_005256190.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 590,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000566165.1",
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"hgvs_c": "n.9C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000463171.1",
"strand": true,
"transcript": "ENST00000566165.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 551,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000741212.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000279622",
"hgvs_c": "n.222-887G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000741212.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs767050",
"effect": "synonymous_variant",
"frequency_reference_population": 0.55428696,
"gene_hgnc_id": 25248,
"gene_symbol": "CRISPLD2",
"gnomad_exomes_ac": 805065,
"gnomad_exomes_af": 0.550827,
"gnomad_exomes_homalt": 224936,
"gnomad_genomes_ac": 89297,
"gnomad_genomes_af": 0.587565,
"gnomad_genomes_homalt": 26795,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 251731,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -4.636,
"pos": 84889253,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_031476.4"
}
]
}