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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: 3-38482193-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38482193&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38482193,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000352511.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ACVR2B",
"gene_hgnc_id": 174,
"hgvs_c": "c.1075-5C>T",
"hgvs_p": null,
"transcript": "NM_001106.4",
"protein_id": "NP_001097.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 512,
"cds_start": -4,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11782,
"mane_select": "ENST00000352511.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ACVR2B",
"gene_hgnc_id": 174,
"hgvs_c": "c.1075-5C>T",
"hgvs_p": null,
"transcript": "ENST00000352511.5",
"protein_id": "ENSP00000340361.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 512,
"cds_start": -4,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11782,
"mane_select": "NM_001106.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ACVR2B",
"gene_hgnc_id": 174,
"hgvs_c": "n.4864-5C>T",
"hgvs_p": null,
"transcript": "ENST00000461232.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 5370,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ACVR2B",
"gene_hgnc_id": 174,
"hgvs_c": "n.1161-5C>T",
"hgvs_p": null,
"transcript": "ENST00000465020.5",
"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": 1666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ACVR2B",
"gene_hgnc_id": 174,
"hgvs_c": "c.1138-5C>T",
"hgvs_p": null,
"transcript": "XM_005265583.4",
"protein_id": "XP_005265640.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 533,
"cds_start": -4,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ACVR2B",
"gene_hgnc_id": 174,
"hgvs_c": "c.1117-5C>T",
"hgvs_p": null,
"transcript": "XM_017007514.2",
"protein_id": "XP_016863003.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 526,
"cds_start": -4,
"cds_end": null,
"cds_length": 1581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ACVR2B",
"gene_hgnc_id": 174,
"hgvs_c": "c.1093-5C>T",
"hgvs_p": null,
"transcript": "XM_017007515.3",
"protein_id": "XP_016863004.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 518,
"cds_start": -4,
"cds_end": null,
"cds_length": 1557,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11595,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ACVR2B",
"gene_hgnc_id": 174,
"hgvs_c": "c.1072-5C>T",
"hgvs_p": null,
"transcript": "XM_017007516.2",
"protein_id": "XP_016863005.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 511,
"cds_start": -4,
"cds_end": null,
"cds_length": 1536,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 14785,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ACVR2B",
"gene_hgnc_id": 174,
"dbsnp": "rs115155428",
"frequency_reference_population": 0.008217365,
"hom_count_reference_population": 69,
"allele_count_reference_population": 13260,
"gnomad_exomes_af": 0.00840299,
"gnomad_genomes_af": 0.00642968,
"gnomad_exomes_ac": 12284,
"gnomad_genomes_ac": 976,
"gnomad_exomes_homalt": 64,
"gnomad_genomes_homalt": 5,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.771,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000232426929095678,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000352511.5",
"gene_symbol": "ACVR2B",
"hgnc_id": 174,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1075-5C>T",
"hgvs_p": null
}
],
"clinvar_disease": " 4, autosomal, visceral,Heterotaxy,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:5",
"phenotype_combined": "not specified|Heterotaxy, visceral, 4, autosomal|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}