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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: 4-109302164-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=109302164&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 109302164,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000399132.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-57+5G>A",
"hgvs_p": null,
"transcript": "NM_198721.4",
"protein_id": "NP_942014.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 654,
"cds_start": -4,
"cds_end": null,
"cds_length": 1965,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7713,
"mane_select": "ENST00000399132.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-57+5G>A",
"hgvs_p": null,
"transcript": "ENST00000399132.6",
"protein_id": "ENSP00000382083.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 654,
"cds_start": -4,
"cds_end": null,
"cds_length": 1965,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7713,
"mane_select": "NM_198721.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-145G>A",
"hgvs_p": null,
"transcript": "ENST00000642955.1",
"protein_id": "ENSP00000495847.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 696,
"cds_start": -4,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-145G>A",
"hgvs_p": null,
"transcript": "NM_001256074.3",
"protein_id": "NP_001243003.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 645,
"cds_start": -4,
"cds_end": null,
"cds_length": 1938,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-145G>A",
"hgvs_p": null,
"transcript": "ENST00000399127.5",
"protein_id": "ENSP00000382078.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 645,
"cds_start": -4,
"cds_end": null,
"cds_length": 1938,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-57+5G>A",
"hgvs_p": null,
"transcript": "NM_032518.4",
"protein_id": "NP_115907.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 642,
"cds_start": -4,
"cds_end": null,
"cds_length": 1929,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-57+5G>A",
"hgvs_p": null,
"transcript": "ENST00000399126.1",
"protein_id": "ENSP00000382077.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 642,
"cds_start": -4,
"cds_end": null,
"cds_length": 1929,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-56-89G>A",
"hgvs_p": null,
"transcript": "ENST00000505591.1",
"protein_id": "ENSP00000422266.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 69,
"cds_start": -4,
"cds_end": null,
"cds_length": 211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "n.-56-89G>A",
"hgvs_p": null,
"transcript": "ENST00000494183.5",
"protein_id": "ENSP00000437131.1",
"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": 4630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "n.357-89G>A",
"hgvs_p": null,
"transcript": "NR_045756.3",
"protein_id": null,
"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": 4921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-57+5G>A",
"hgvs_p": null,
"transcript": "XM_011532333.3",
"protein_id": "XP_011530635.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 696,
"cds_start": -4,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-56-89G>A",
"hgvs_p": null,
"transcript": "XM_011532334.3",
"protein_id": "XP_011530636.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 696,
"cds_start": -4,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"hgvs_c": "c.-56-89G>A",
"hgvs_p": null,
"transcript": "XM_011532335.3",
"protein_id": "XP_011530637.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 696,
"cds_start": -4,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL25A1",
"gene_hgnc_id": 18603,
"dbsnp": "rs1859143",
"frequency_reference_population": 0.46747383,
"hom_count_reference_population": 119683,
"allele_count_reference_population": 489073,
"gnomad_exomes_af": 0.454289,
"gnomad_genomes_af": 0.544949,
"gnomad_exomes_ac": 406159,
"gnomad_genomes_ac": 82914,
"gnomad_exomes_homalt": 94634,
"gnomad_genomes_homalt": 25049,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.48495951294898987,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_ADA",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.636,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.46,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.484959503604159,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BA1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000399132.6",
"gene_symbol": "COL25A1",
"hgnc_id": 18603,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.-57+5G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}