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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: 2-219539785-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=219539785&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CHPF",
"hgnc_id": 24291,
"hgvs_c": "c.1926G>A",
"hgvs_p": "p.Met642Ile",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_024536.6",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 32,
"alphamissense_prediction": null,
"alphamissense_score": 0.1696,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.58,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.06195220351219177,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 775,
"aa_ref": "M",
"aa_start": 642,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3028,
"cdna_start": 2197,
"cds_end": null,
"cds_length": 2328,
"cds_start": 1926,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_024536.6",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "c.1926G>A",
"hgvs_p": "p.Met642Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000243776.11",
"protein_coding": true,
"protein_id": "NP_078812.3",
"strand": false,
"transcript": "NM_024536.6",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 775,
"aa_ref": "M",
"aa_start": 642,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3028,
"cdna_start": 2197,
"cds_end": null,
"cds_length": 2328,
"cds_start": 1926,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000243776.11",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "c.1926G>A",
"hgvs_p": "p.Met642Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024536.6",
"protein_coding": true,
"protein_id": "ENSP00000243776.6",
"strand": false,
"transcript": "ENST00000243776.11",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 767,
"aa_ref": "M",
"aa_start": 634,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2766,
"cdna_start": 1959,
"cds_end": null,
"cds_length": 2304,
"cds_start": 1902,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000691864.1",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "c.1902G>A",
"hgvs_p": "p.Met634Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509104.1",
"strand": false,
"transcript": "ENST00000691864.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 749,
"aa_ref": "M",
"aa_start": 616,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2964,
"cdna_start": 2128,
"cds_end": null,
"cds_length": 2250,
"cds_start": 1848,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000919936.1",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "c.1848G>A",
"hgvs_p": "p.Met616Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589995.1",
"strand": false,
"transcript": "ENST00000919936.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 715,
"aa_ref": "M",
"aa_start": 582,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2797,
"cdna_start": 1966,
"cds_end": null,
"cds_length": 2148,
"cds_start": 1746,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000888378.1",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "c.1746G>A",
"hgvs_p": "p.Met582Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558437.1",
"strand": false,
"transcript": "ENST00000888378.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 613,
"aa_ref": "M",
"aa_start": 480,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2628,
"cdna_start": 1797,
"cds_end": null,
"cds_length": 1842,
"cds_start": 1440,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001195731.2",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "c.1440G>A",
"hgvs_p": "p.Met480Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001182660.2",
"strand": false,
"transcript": "NM_001195731.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 613,
"aa_ref": "M",
"aa_start": 480,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2210,
"cdna_start": 1797,
"cds_end": null,
"cds_length": 1842,
"cds_start": 1440,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000535926.3",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "c.1440G>A",
"hgvs_p": "p.Met480Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000445571.1",
"strand": false,
"transcript": "ENST00000535926.3",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 484,
"aa_ref": "M",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2524,
"cdna_start": 1693,
"cds_end": null,
"cds_length": 1455,
"cds_start": 1053,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011511838.4",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "c.1053G>A",
"hgvs_p": "p.Met351Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011510140.1",
"strand": false,
"transcript": "XM_011511838.4",
"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": 2871,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000688634.1",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "n.*1110G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509339.1",
"strand": false,
"transcript": "ENST00000688634.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3280,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000693236.1",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "n.2473G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000693236.1",
"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": 2871,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000688634.1",
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"hgvs_c": "n.*1110G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509339.1",
"strand": false,
"transcript": "ENST00000688634.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs142262640",
"effect": "missense_variant",
"frequency_reference_population": 0.00001983431,
"gene_hgnc_id": 24291,
"gene_symbol": "CHPF",
"gnomad_exomes_ac": 11,
"gnomad_exomes_af": 0.0000075285,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 21,
"gnomad_genomes_af": 0.000137929,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.779,
"pos": 219539785,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.066,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_024536.6"
}
]
}