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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: 2-168935354-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=168935354&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 168935354,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000650372.1",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2886A>G",
"hgvs_p": "p.Ala962Ala",
"transcript": "NM_003742.4",
"protein_id": "NP_003733.2",
"transcript_support_level": null,
"aa_start": 962,
"aa_end": null,
"aa_length": 1321,
"cds_start": 2886,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 3013,
"cdna_end": null,
"cdna_length": 6934,
"mane_select": "ENST00000650372.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2886A>G",
"hgvs_p": "p.Ala962Ala",
"transcript": "ENST00000650372.1",
"protein_id": "ENSP00000497931.1",
"transcript_support_level": null,
"aa_start": 962,
"aa_end": null,
"aa_length": 1321,
"cds_start": 2886,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 3013,
"cdna_end": null,
"cdna_length": 6934,
"mane_select": "NM_003742.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1203A>G",
"hgvs_p": "p.Ala401Ala",
"transcript": "ENST00000649448.1",
"protein_id": "ENSP00000497165.1",
"transcript_support_level": null,
"aa_start": 401,
"aa_end": null,
"aa_length": 780,
"cds_start": 1203,
"cds_end": null,
"cds_length": 2343,
"cdna_start": 1203,
"cdna_end": null,
"cdna_length": 2983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2988A>G",
"hgvs_p": "p.Ala996Ala",
"transcript": "XM_011512078.3",
"protein_id": "XP_011510380.1",
"transcript_support_level": null,
"aa_start": 996,
"aa_end": null,
"aa_length": 1355,
"cds_start": 2988,
"cds_end": null,
"cds_length": 4068,
"cdna_start": 3115,
"cdna_end": null,
"cdna_length": 4974,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2928A>G",
"hgvs_p": "p.Ala976Ala",
"transcript": "XM_006712817.4",
"protein_id": "XP_006712880.1",
"transcript_support_level": null,
"aa_start": 976,
"aa_end": null,
"aa_length": 1335,
"cds_start": 2928,
"cds_end": null,
"cds_length": 4008,
"cdna_start": 3055,
"cdna_end": null,
"cdna_length": 4181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2988A>G",
"hgvs_p": "p.Ala996Ala",
"transcript": "XM_017005165.2",
"protein_id": "XP_016860654.1",
"transcript_support_level": null,
"aa_start": 996,
"aa_end": null,
"aa_length": 1314,
"cds_start": 2988,
"cds_end": null,
"cds_length": 3945,
"cdna_start": 3115,
"cdna_end": null,
"cdna_length": 4287,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2217A>G",
"hgvs_p": "p.Ala739Ala",
"transcript": "XM_017005166.2",
"protein_id": "XP_016860655.1",
"transcript_support_level": null,
"aa_start": 739,
"aa_end": null,
"aa_length": 1098,
"cds_start": 2217,
"cds_end": null,
"cds_length": 3297,
"cdna_start": 2310,
"cdna_end": null,
"cdna_length": 3436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1671A>G",
"hgvs_p": "p.Ala557Ala",
"transcript": "XM_017005167.2",
"protein_id": "XP_016860656.1",
"transcript_support_level": null,
"aa_start": 557,
"aa_end": null,
"aa_length": 916,
"cds_start": 1671,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 1867,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": null,
"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": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "n.*1356A>G",
"hgvs_p": null,
"transcript": "ENST00000439188.1",
"protein_id": "ENSP00000416058.1",
"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": 2822,
"mane_select": null,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "n.51A>G",
"hgvs_p": null,
"transcript": "ENST00000647920.1",
"protein_id": "ENSP00000497947.1",
"transcript_support_level": null,
"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": 452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "n.*1356A>G",
"hgvs_p": null,
"transcript": "ENST00000439188.1",
"protein_id": "ENSP00000416058.1",
"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": 2822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.*97A>G",
"hgvs_p": null,
"transcript": "XM_011512080.3",
"protein_id": "XP_011510382.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 936,
"cds_start": -4,
"cds_end": null,
"cds_length": 2811,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"dbsnp": "rs201087979",
"frequency_reference_population": 0.00007063136,
"hom_count_reference_population": 0,
"allele_count_reference_population": 114,
"gnomad_exomes_af": 0.00003968,
"gnomad_genomes_af": 0.000367642,
"gnomad_exomes_ac": 58,
"gnomad_genomes_ac": 56,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"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,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.7,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.431,
"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": "ENST00000650372.1",
"gene_symbol": "ABCB11",
"hgnc_id": 42,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2886A>G",
"hgvs_p": "p.Ala962Ala"
}
],
"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:2 LB:2",
"phenotype_combined": "Progressive familial intrahepatic cholestasis type 2|not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}