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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: 17-50192029-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50192029&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 50192029,
"ref": "G",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000225964.10",
"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": 51,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.1984-5C>A",
"hgvs_p": null,
"transcript": "NM_000088.4",
"protein_id": "NP_000079.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1464,
"cds_start": -4,
"cds_end": null,
"cds_length": 4395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5914,
"mane_select": "ENST00000225964.10",
"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": 51,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.1984-5C>A",
"hgvs_p": null,
"transcript": "ENST00000225964.10",
"protein_id": "ENSP00000225964.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1464,
"cds_start": -4,
"cds_end": null,
"cds_length": 4395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5914,
"mane_select": "NM_000088.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "n.411C>A",
"hgvs_p": null,
"transcript": "ENST00000504289.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "n.333-5C>A",
"hgvs_p": null,
"transcript": "ENST00000476387.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 600,
"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": 48,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.1786-5C>A",
"hgvs_p": null,
"transcript": "XM_011524341.2",
"protein_id": "XP_011522643.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1398,
"cds_start": -4,
"cds_end": null,
"cds_length": 4197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5716,
"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": 49,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.1984-5C>A",
"hgvs_p": null,
"transcript": "XM_005257058.5",
"protein_id": "XP_005257115.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1374,
"cds_start": -4,
"cds_end": null,
"cds_length": 4125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5644,
"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": 38,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"hgvs_c": "c.1066-5C>A",
"hgvs_p": null,
"transcript": "XM_005257059.5",
"protein_id": "XP_005257116.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": -4,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL1A1",
"gene_hgnc_id": 2197,
"dbsnp": "rs66592376",
"frequency_reference_population": 0.003921138,
"hom_count_reference_population": 19,
"allele_count_reference_population": 6321,
"gnomad_exomes_af": 0.00403283,
"gnomad_genomes_af": 0.00285031,
"gnomad_exomes_ac": 5887,
"gnomad_genomes_ac": 434,
"gnomad_exomes_homalt": 18,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.75,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.23399999737739563,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.736,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0022468727699856,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000225964.10",
"gene_symbol": "COL1A1",
"hgnc_id": 2197,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1984-5C>A",
"hgvs_p": null
}
],
"clinvar_disease": " arthrochalasia type,COL1A1-related disorder,Cardiovascular phenotype,Connective tissue disorder,Ehlers-Danlos syndrome,Ehlers-Danlos/osteogenesis imperfecta syndrome,Infantile cortical hyperostosis,Osteogenesis imperfecta,Osteogenesis imperfecta type I,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:6 B:9",
"phenotype_combined": "not specified|Connective tissue disorder|Infantile cortical hyperostosis|Osteogenesis imperfecta|Ehlers-Danlos syndrome|Ehlers-Danlos syndrome, arthrochalasia type|Cardiovascular phenotype|Ehlers-Danlos/osteogenesis imperfecta syndrome|not provided|Osteogenesis imperfecta type I|COL1A1-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}