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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: 12-100493324-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=100493324&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 100493324,
"ref": "A",
"alt": "G",
"effect": "start_lost",
"transcript": "ENST00000392986.8",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001206979.2",
"protein_id": "NP_001193908.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 476,
"cds_start": 1,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 2739,
"mane_select": "ENST00000392986.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000392986.8",
"protein_id": "ENSP00000376712.3",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 476,
"cds_start": 1,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 2739,
"mane_select": "NM_001206979.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000548884.5",
"protein_id": "ENSP00000448506.1",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 472,
"cds_start": 1,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 2884,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000549996.5",
"protein_id": "ENSP00000448978.1",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 425,
"cds_start": 1,
"cds_end": null,
"cds_length": 1278,
"cdna_start": 334,
"cdna_end": null,
"cdna_length": 1633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "n.1A>G",
"hgvs_p": null,
"transcript": "ENST00000321046.9",
"protein_id": "ENSP00000315442.5",
"transcript_support_level": 1,
"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": 1779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001206977.2",
"protein_id": "NP_001193906.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 476,
"cds_start": 1,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 551,
"cdna_end": null,
"cdna_length": 2906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000648861.1",
"protein_id": "ENSP00000496908.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 476,
"cds_start": 1,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 466,
"cdna_end": null,
"cdna_length": 2274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_005123.4",
"protein_id": "NP_005114.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 472,
"cds_start": 1,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 2727,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001206978.2",
"protein_id": "NP_001193907.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 425,
"cds_start": 1,
"cds_end": null,
"cds_length": 1278,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 2586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000546380.1",
"protein_id": "ENSP00000446760.1",
"transcript_support_level": 3,
"aa_start": 1,
"aa_end": null,
"aa_length": 45,
"cds_start": 1,
"cds_end": null,
"cds_length": 138,
"cdna_start": 295,
"cdna_end": null,
"cdna_length": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000649582.1",
"protein_id": "ENSP00000496824.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 45,
"cds_start": 1,
"cds_end": null,
"cds_length": 138,
"cdna_start": 524,
"cdna_end": null,
"cdna_length": 810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_011539040.3",
"protein_id": "XP_011537342.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 476,
"cds_start": 1,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 1395,
"cdna_end": null,
"cdna_length": 3750,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_047429943.1",
"protein_id": "XP_047285899.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 472,
"cds_start": 1,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 551,
"cdna_end": null,
"cdna_length": 2894,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_047429944.1",
"protein_id": "XP_047285900.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 274,
"cds_start": 1,
"cds_end": null,
"cds_length": 825,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 1312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "n.1A>G",
"hgvs_p": null,
"transcript": "ENST00000548621.2",
"protein_id": "ENSP00000446584.1",
"transcript_support_level": 3,
"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": 720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"hgvs_c": "n.384A>G",
"hgvs_p": null,
"transcript": "NR_135146.2",
"protein_id": null,
"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": 2732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NR1H4",
"gene_hgnc_id": 7967,
"dbsnp": "rs138943609",
"frequency_reference_population": 0.00026928342,
"hom_count_reference_population": 0,
"allele_count_reference_population": 413,
"gnomad_exomes_af": 0.00027288,
"gnomad_genomes_af": 0.000236621,
"gnomad_exomes_ac": 377,
"gnomad_genomes_ac": 36,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09134316444396973,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.487,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 0.45,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Supporting,BS1_Supporting",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PVS1_Supporting",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000392986.8",
"gene_symbol": "NR1H4",
"hgnc_id": 7967,
"effects": [
"start_lost"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?"
}
],
"clinvar_disease": " 5, progressive familial intrahepatic,Cholestasis,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|Cholestasis, progressive familial intrahepatic, 5",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}