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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: 20-18542289-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=18542289&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 18542289,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000650089.1",
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1405-7C>T",
"hgvs_p": null,
"transcript": "NM_006363.6",
"protein_id": "NP_006354.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 767,
"cds_start": -4,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3026,
"mane_select": "ENST00000650089.1",
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1405-7C>T",
"hgvs_p": null,
"transcript": "ENST00000650089.1",
"protein_id": "ENSP00000497473.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 767,
"cds_start": -4,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3026,
"mane_select": "NM_006363.6",
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1405-7C>T",
"hgvs_p": null,
"transcript": "ENST00000336714.8",
"protein_id": "ENSP00000338844.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 767,
"cds_start": -4,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3464,
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1405-7C>T",
"hgvs_p": null,
"transcript": "ENST00000377465.6",
"protein_id": "ENSP00000366685.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 767,
"cds_start": -4,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3351,
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1405-7C>T",
"hgvs_p": null,
"transcript": "NM_001172745.3",
"protein_id": "NP_001166216.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 767,
"cds_start": -4,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3351,
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1405-7C>T",
"hgvs_p": null,
"transcript": "NM_032985.6",
"protein_id": "NP_116780.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 767,
"cds_start": -4,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3044,
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1405-7C>T",
"hgvs_p": null,
"transcript": "NM_032986.5",
"protein_id": "NP_116781.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 767,
"cds_start": -4,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3115,
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1405-7C>T",
"hgvs_p": null,
"transcript": "ENST00000262544.6",
"protein_id": "ENSP00000262544.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 767,
"cds_start": -4,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3176,
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1351-7C>T",
"hgvs_p": null,
"transcript": "NM_001172746.3",
"protein_id": "NP_001166217.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 749,
"cds_start": -4,
"cds_end": null,
"cds_length": 2250,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2990,
"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": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.1351-7C>T",
"hgvs_p": null,
"transcript": "ENST00000643747.1",
"protein_id": "ENSP00000496460.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 749,
"cds_start": -4,
"cds_end": null,
"cds_length": 2250,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"hgvs_c": "c.-79C>T",
"hgvs_p": null,
"transcript": "ENST00000422877.1",
"protein_id": "ENSP00000409882.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 246,
"cds_start": -4,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SEC23B",
"gene_hgnc_id": 10702,
"dbsnp": "rs2273525",
"frequency_reference_population": 0.08591447,
"hom_count_reference_population": 8525,
"allele_count_reference_population": 138612,
"gnomad_exomes_af": 0.0848446,
"gnomad_genomes_af": 0.0961864,
"gnomad_exomes_ac": 123973,
"gnomad_genomes_ac": 14639,
"gnomad_exomes_homalt": 7644,
"gnomad_genomes_homalt": 881,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.699999988079071,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.0020000000949949026,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.7,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.395,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000200318272882703,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000650089.1",
"gene_symbol": "SEC23B",
"hgnc_id": 10702,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1405-7C>T",
"hgvs_p": null
}
],
"clinvar_disease": " type II,Congenital dyserythropoietic anemia,Cowden syndrome 7,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "not specified|Congenital dyserythropoietic anemia, type II|Congenital dyserythropoietic anemia, type II;Cowden syndrome 7|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}