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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: 2-168930818-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=168930818&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 168930818,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_003742.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.3258A>G",
"hgvs_p": "p.Thr1086Thr",
"transcript": "NM_003742.4",
"protein_id": "NP_003733.2",
"transcript_support_level": null,
"aa_start": 1086,
"aa_end": null,
"aa_length": 1321,
"cds_start": 3258,
"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": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.3258A>G",
"hgvs_p": "p.Thr1086Thr",
"transcript": "ENST00000650372.1",
"protein_id": "ENSP00000497931.1",
"transcript_support_level": null,
"aa_start": 1086,
"aa_end": null,
"aa_length": 1321,
"cds_start": 3258,
"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": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.3300A>G",
"hgvs_p": "p.Thr1100Thr",
"transcript": "ENST00000858973.1",
"protein_id": "ENSP00000529032.1",
"transcript_support_level": null,
"aa_start": 1100,
"aa_end": null,
"aa_length": 1335,
"cds_start": 3300,
"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": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.3153A>G",
"hgvs_p": "p.Thr1051Thr",
"transcript": "ENST00000858972.1",
"protein_id": "ENSP00000529031.1",
"transcript_support_level": null,
"aa_start": 1051,
"aa_end": null,
"aa_length": 1286,
"cds_start": 3153,
"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": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2991A>G",
"hgvs_p": "p.Thr997Thr",
"transcript": "ENST00000858971.1",
"protein_id": "ENSP00000529030.1",
"transcript_support_level": null,
"aa_start": 997,
"aa_end": null,
"aa_length": 1232,
"cds_start": 2991,
"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": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.1575A>G",
"hgvs_p": "p.Thr525Thr",
"transcript": "ENST00000649448.1",
"protein_id": "ENSP00000497165.1",
"transcript_support_level": null,
"aa_start": 525,
"aa_end": null,
"aa_length": 780,
"cds_start": 1575,
"cds_end": null,
"cds_length": 2343,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000649448.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.3360A>G",
"hgvs_p": "p.Thr1120Thr",
"transcript": "XM_011512078.3",
"protein_id": "XP_011510380.1",
"transcript_support_level": null,
"aa_start": 1120,
"aa_end": null,
"aa_length": 1355,
"cds_start": 3360,
"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": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.3300A>G",
"hgvs_p": "p.Thr1100Thr",
"transcript": "XM_006712817.4",
"protein_id": "XP_006712880.1",
"transcript_support_level": null,
"aa_start": 1100,
"aa_end": null,
"aa_length": 1335,
"cds_start": 3300,
"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": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.3360A>G",
"hgvs_p": "p.Thr1120Thr",
"transcript": "XM_017005165.2",
"protein_id": "XP_016860654.1",
"transcript_support_level": null,
"aa_start": 1120,
"aa_end": null,
"aa_length": 1314,
"cds_start": 3360,
"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": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2589A>G",
"hgvs_p": "p.Thr863Thr",
"transcript": "XM_017005166.2",
"protein_id": "XP_016860655.1",
"transcript_support_level": null,
"aa_start": 863,
"aa_end": null,
"aa_length": 1098,
"cds_start": 2589,
"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": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "c.2043A>G",
"hgvs_p": "p.Thr681Thr",
"transcript": "XM_017005167.2",
"protein_id": "XP_016860656.1",
"transcript_support_level": null,
"aa_start": 681,
"aa_end": null,
"aa_length": 916,
"cds_start": 2043,
"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"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "n.*1728A>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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000439188.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"hgvs_c": "n.*1728A>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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000439188.1"
}
],
"gene_symbol": "ABCB11",
"gene_hgnc_id": 42,
"dbsnp": "rs11568359",
"frequency_reference_population": 0.0045367377,
"hom_count_reference_population": 268,
"allele_count_reference_population": 7310,
"gnomad_exomes_af": 0.00244616,
"gnomad_genomes_af": 0.0245682,
"gnomad_exomes_ac": 3569,
"gnomad_genomes_ac": 3741,
"gnomad_exomes_homalt": 135,
"gnomad_genomes_homalt": 133,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6100000143051147,
"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": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.071,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_003742.4",
"gene_symbol": "ABCB11",
"hgnc_id": 42,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3258A>G",
"hgvs_p": "p.Thr1086Thr"
}
],
"clinvar_disease": "Progressive familial intrahepatic cholestasis type 2,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|Progressive familial intrahepatic cholestasis type 2|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}