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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: 2-168976604-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=168976604&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 168976604,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_003742.4",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1281C>T",
"hgvs_p": "p.Phe427Phe",
"transcript": "NM_003742.4",
"protein_id": "NP_003733.2",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 1321,
"cds_start": 1281,
"cds_end": null,
"cds_length": 3966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000650372.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003742.4"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1281C>T",
"hgvs_p": "p.Phe427Phe",
"transcript": "ENST00000650372.1",
"protein_id": "ENSP00000497931.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 1321,
"cds_start": 1281,
"cds_end": null,
"cds_length": 3966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003742.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000650372.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1323C>T",
"hgvs_p": "p.Phe441Phe",
"transcript": "ENST00000858973.1",
"protein_id": "ENSP00000529032.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 1335,
"cds_start": 1323,
"cds_end": null,
"cds_length": 4008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858973.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1281C>T",
"hgvs_p": "p.Phe427Phe",
"transcript": "ENST00000858972.1",
"protein_id": "ENSP00000529031.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 1286,
"cds_start": 1281,
"cds_end": null,
"cds_length": 3861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858972.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1281C>T",
"hgvs_p": "p.Phe427Phe",
"transcript": "ENST00000858971.1",
"protein_id": "ENSP00000529030.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 1232,
"cds_start": 1281,
"cds_end": null,
"cds_length": 3699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858971.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1383C>T",
"hgvs_p": "p.Phe461Phe",
"transcript": "XM_011512078.3",
"protein_id": "XP_011510380.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 1355,
"cds_start": 1383,
"cds_end": null,
"cds_length": 4068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512078.3"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1323C>T",
"hgvs_p": "p.Phe441Phe",
"transcript": "XM_006712817.4",
"protein_id": "XP_006712880.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 1335,
"cds_start": 1323,
"cds_end": null,
"cds_length": 4008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006712817.4"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1383C>T",
"hgvs_p": "p.Phe461Phe",
"transcript": "XM_017005165.2",
"protein_id": "XP_016860654.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 1314,
"cds_start": 1383,
"cds_end": null,
"cds_length": 3945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005165.2"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.612C>T",
"hgvs_p": "p.Phe204Phe",
"transcript": "XM_017005166.2",
"protein_id": "XP_016860655.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 1098,
"cds_start": 612,
"cds_end": null,
"cds_length": 3297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005166.2"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1383C>T",
"hgvs_p": "p.Phe461Phe",
"transcript": "XM_011512080.3",
"protein_id": "XP_011510382.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 936,
"cds_start": 1383,
"cds_end": null,
"cds_length": 2811,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512080.3"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.66C>T",
"hgvs_p": "p.Phe22Phe",
"transcript": "XM_017005167.2",
"protein_id": "XP_016860656.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 916,
"cds_start": 66,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005167.2"
}
],
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"dbsnp": "rs11568360",
"frequency_reference_population": 0.00021420264,
"hom_count_reference_population": 0,
"allele_count_reference_population": 344,
"gnomad_exomes_af": 0.000140327,
"gnomad_genomes_af": 0.000919782,
"gnomad_exomes_ac": 204,
"gnomad_genomes_ac": 140,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5600000023841858,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.538,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6,BP7",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_003742.4",
"gene_symbol": "ABCB11",
"hgnc_id": 42,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1281C>T",
"hgvs_p": "p.Phe427Phe"
}
],
"clinvar_disease": "Progressive familial intrahepatic cholestasis type 2,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "not specified|not provided|Progressive familial intrahepatic cholestasis type 2",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}