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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: 1-161222526-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=161222526&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 161222526,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000367990.7",
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "c.186-4C>T",
"hgvs_p": null,
"transcript": "NM_001643.2",
"protein_id": "NP_001634.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 100,
"cds_start": -4,
"cds_end": null,
"cds_length": 303,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 474,
"mane_select": "ENST00000367990.7",
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "c.186-4C>T",
"hgvs_p": null,
"transcript": "ENST00000367990.7",
"protein_id": "ENSP00000356969.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 100,
"cds_start": -4,
"cds_end": null,
"cds_length": 303,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 474,
"mane_select": "NM_001643.2",
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "c.186-4C>T",
"hgvs_p": null,
"transcript": "ENST00000463273.6",
"protein_id": "ENSP00000476740.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 100,
"cds_start": -4,
"cds_end": null,
"cds_length": 303,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 602,
"mane_select": null,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "c.186-4C>T",
"hgvs_p": null,
"transcript": "ENST00000470459.6",
"protein_id": "ENSP00000477031.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 82,
"cds_start": -4,
"cds_end": null,
"cds_length": 249,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 416,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "c.53-4C>T",
"hgvs_p": null,
"transcript": "ENST00000491350.1",
"protein_id": "ENSP00000477353.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 27,
"cds_start": -4,
"cds_end": null,
"cds_length": 84,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 263,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "c.285-4C>T",
"hgvs_p": null,
"transcript": "ENST00000464492.5",
"protein_id": "ENSP00000476911.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 133,
"cds_start": -4,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 530,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "c.186-4C>T",
"hgvs_p": null,
"transcript": "ENST00000469730.2",
"protein_id": "ENSP00000476605.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 65,
"cds_start": -4,
"cds_end": null,
"cds_length": 200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 265,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "c.42-4C>T",
"hgvs_p": null,
"transcript": "ENST00000463812.1",
"protein_id": "ENSP00000476890.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 52,
"cds_start": -4,
"cds_end": null,
"cds_length": 159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 401,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "c.42-4C>T",
"hgvs_p": null,
"transcript": "ENST00000468465.5",
"protein_id": "ENSP00000476662.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 52,
"cds_start": -4,
"cds_end": null,
"cds_length": 159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 421,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "n.697-4C>T",
"hgvs_p": null,
"transcript": "ENST00000481413.1",
"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": 927,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"hgvs_c": "n.*183-4C>T",
"hgvs_p": null,
"transcript": "ENST00000481511.5",
"protein_id": "ENSP00000477054.1",
"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": 655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "APOA2",
"gene_hgnc_id": 601,
"dbsnp": "rs6413453",
"frequency_reference_population": 0.110888325,
"hom_count_reference_population": 10689,
"allele_count_reference_population": 178687,
"gnomad_exomes_af": 0.11338,
"gnomad_genomes_af": 0.0870111,
"gnomad_exomes_ac": 165438,
"gnomad_genomes_ac": 13249,
"gnomad_exomes_homalt": 9987,
"gnomad_genomes_homalt": 702,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7900000214576721,
"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": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.116,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000216412400318353,
"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": "ENST00000367990.7",
"gene_symbol": "APOA2",
"hgnc_id": 601,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.186-4C>T",
"hgvs_p": null
}
],
"clinvar_disease": "APOA2-related disorder,Apolipoprotein A-II deficiency,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Apolipoprotein A-II deficiency|not provided|APOA2-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}