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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: 1-223625884-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=223625884&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CAPN8",
"hgnc_id": 1485,
"hgvs_c": "c.734C>A",
"hgvs_p": "p.Ser245Tyr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_001143962.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 856143,
"alphamissense_prediction": null,
"alphamissense_score": 0.1114,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.43,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0004118680953979492,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 703,
"aa_ref": "S",
"aa_start": 245,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2387,
"cdna_start": 789,
"cds_end": null,
"cds_length": 2112,
"cds_start": 734,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001143962.2",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.734C>A",
"hgvs_p": "p.Ser245Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000366872.10",
"protein_coding": true,
"protein_id": "NP_001137434.1",
"strand": false,
"transcript": "NM_001143962.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 703,
"aa_ref": "S",
"aa_start": 245,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2387,
"cdna_start": 789,
"cds_end": null,
"cds_length": 2112,
"cds_start": 734,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000366872.10",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.734C>A",
"hgvs_p": "p.Ser245Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001143962.2",
"protein_coding": true,
"protein_id": "ENSP00000355837.6",
"strand": false,
"transcript": "ENST00000366872.10",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 699,
"aa_ref": "S",
"aa_start": 245,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2375,
"cdna_start": 789,
"cds_end": null,
"cds_length": 2100,
"cds_start": 734,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000871507.1",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.734C>A",
"hgvs_p": "p.Ser245Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541566.1",
"strand": false,
"transcript": "ENST00000871507.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 639,
"aa_ref": "S",
"aa_start": 245,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2197,
"cdna_start": 789,
"cds_end": null,
"cds_length": 1920,
"cds_start": 734,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000961029.1",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.734C>A",
"hgvs_p": "p.Ser245Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000631088.1",
"strand": false,
"transcript": "ENST00000961029.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 381,
"aa_ref": "S",
"aa_start": 245,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2596,
"cdna_start": 811,
"cds_end": null,
"cds_length": 1146,
"cds_start": 734,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000366873.6",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.734C>A",
"hgvs_p": "p.Ser245Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000355838.2",
"strand": false,
"transcript": "ENST00000366873.6",
"transcript_support_level": 5
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 172,
"aa_ref": "S",
"aa_start": 117,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 710,
"cdna_start": 352,
"cds_end": null,
"cds_length": 519,
"cds_start": 350,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000465098.1",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.350C>A",
"hgvs_p": "p.Ser117Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000435953.1",
"strand": false,
"transcript": "ENST00000465098.1",
"transcript_support_level": 3
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 542,
"aa_ref": "S",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1891,
"cdna_start": 293,
"cds_end": null,
"cds_length": 1629,
"cds_start": 251,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017001265.2",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.251C>A",
"hgvs_p": "p.Ser84Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856754.1",
"strand": false,
"transcript": "XM_017001265.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 476,
"aa_ref": "P",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1781,
"cdna_start": 269,
"cds_end": null,
"cds_length": 1431,
"cds_start": 139,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_017001266.2",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.139C>A",
"hgvs_p": "p.Pro47Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856755.1",
"strand": false,
"transcript": "XM_017001266.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 447,
"aa_ref": "S",
"aa_start": 245,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1496,
"cdna_start": 789,
"cds_end": null,
"cds_length": 1344,
"cds_start": 734,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_017001267.3",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.734C>A",
"hgvs_p": "p.Ser245Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856756.1",
"strand": false,
"transcript": "XM_017001267.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 381,
"aa_ref": "S",
"aa_start": 245,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2142,
"cdna_start": 789,
"cds_end": null,
"cds_length": 1146,
"cds_start": 734,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_017001268.2",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "c.734C>A",
"hgvs_p": "p.Ser245Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856757.1",
"strand": false,
"transcript": "XM_017001268.2",
"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": 884,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000467384.6",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "n.*531C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000434013.1",
"strand": false,
"transcript": "ENST00000467384.6",
"transcript_support_level": 5
},
{
"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": 884,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000467384.6",
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"hgvs_c": "n.*531C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000434013.1",
"strand": false,
"transcript": "ENST00000467384.6",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs35539373",
"effect": "missense_variant",
"frequency_reference_population": 0.552647,
"gene_hgnc_id": 1485,
"gene_symbol": "CAPN8",
"gnomad_exomes_ac": 769220,
"gnomad_exomes_af": 0.550565,
"gnomad_exomes_homalt": 213958,
"gnomad_genomes_ac": 86923,
"gnomad_genomes_af": 0.571779,
"gnomad_genomes_homalt": 25373,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 239331,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.996,
"pos": 223625884,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.387,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_001143962.2"
}
]
}