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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: 16-31091247-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=31091247&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 31091247,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_024006.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.379G>A",
"hgvs_p": "p.Val127Met",
"transcript": "NM_024006.6",
"protein_id": "NP_076869.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 163,
"cds_start": 379,
"cds_end": null,
"cds_length": 492,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 840,
"mane_select": "ENST00000394975.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.379G>A",
"hgvs_p": "p.Val127Met",
"transcript": "ENST00000394975.3",
"protein_id": "ENSP00000378426.2",
"transcript_support_level": 1,
"aa_start": 127,
"aa_end": null,
"aa_length": 163,
"cds_start": 379,
"cds_end": null,
"cds_length": 492,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 840,
"mane_select": "NM_024006.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.461G>A",
"hgvs_p": "p.Arg154His",
"transcript": "ENST00000319788.11",
"protein_id": "ENSP00000326135.7",
"transcript_support_level": 1,
"aa_start": 154,
"aa_end": null,
"aa_length": 156,
"cds_start": 461,
"cds_end": null,
"cds_length": 471,
"cdna_start": 672,
"cdna_end": null,
"cdna_length": 1077,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.269G>A",
"hgvs_p": "p.Arg90His",
"transcript": "ENST00000354895.4",
"protein_id": "ENSP00000346969.4",
"transcript_support_level": 1,
"aa_start": 90,
"aa_end": null,
"aa_length": 92,
"cds_start": 269,
"cds_end": null,
"cds_length": 279,
"cdna_start": 496,
"cdna_end": null,
"cdna_length": 901,
"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": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255439",
"gene_hgnc_id": null,
"hgvs_c": "n.250G>A",
"hgvs_p": null,
"transcript": "ENST00000533518.5",
"protein_id": "ENSP00000433035.1",
"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": 2362,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255439",
"gene_hgnc_id": null,
"hgvs_c": "c.283+2065G>A",
"hgvs_p": null,
"transcript": "ENST00000529564.1",
"protein_id": "ENSP00000431371.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 165,
"cds_start": -4,
"cds_end": null,
"cds_length": 498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.463G>A",
"hgvs_p": "p.Val155Met",
"transcript": "NM_001311311.2",
"protein_id": "NP_001298240.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 191,
"cds_start": 463,
"cds_end": null,
"cds_length": 576,
"cdna_start": 531,
"cdna_end": null,
"cdna_length": 924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.476G>A",
"hgvs_p": "p.Arg159His",
"transcript": "ENST00000498155.1",
"protein_id": "ENSP00000417662.1",
"transcript_support_level": 5,
"aa_start": 159,
"aa_end": null,
"aa_length": 161,
"cds_start": 476,
"cds_end": null,
"cds_length": 486,
"cdna_start": 798,
"cdna_end": null,
"cdna_length": 870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.473G>A",
"hgvs_p": "p.Arg158His",
"transcript": "ENST00000394971.7",
"protein_id": "ENSP00000378422.3",
"transcript_support_level": 5,
"aa_start": 158,
"aa_end": null,
"aa_length": 160,
"cds_start": 473,
"cds_end": null,
"cds_length": 483,
"cdna_start": 521,
"cdna_end": null,
"cdna_length": 664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.440G>A",
"hgvs_p": "p.Arg147His",
"transcript": "ENST00000300851.10",
"protein_id": "ENSP00000300851.6",
"transcript_support_level": 2,
"aa_start": 147,
"aa_end": null,
"aa_length": 149,
"cds_start": 440,
"cds_end": null,
"cds_length": 450,
"cdna_start": 471,
"cdna_end": null,
"cdna_length": 876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.269G>A",
"hgvs_p": "p.Arg90His",
"transcript": "NM_206824.3",
"protein_id": "NP_996560.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 92,
"cds_start": 269,
"cds_end": null,
"cds_length": 279,
"cdna_start": 337,
"cdna_end": null,
"cdna_length": 730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.64G>A",
"hgvs_p": "p.Val22Met",
"transcript": "ENST00000472468.1",
"protein_id": "ENSP00000458994.1",
"transcript_support_level": 2,
"aa_start": 22,
"aa_end": null,
"aa_length": 42,
"cds_start": 64,
"cds_end": null,
"cds_length": 129,
"cdna_start": 396,
"cdna_end": null,
"cdna_length": 461,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"hgvs_c": "c.*63G>A",
"hgvs_p": null,
"transcript": "ENST00000420057.2",
"protein_id": "ENSP00000437064.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 91,
"cds_start": -4,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255439",
"gene_hgnc_id": null,
"hgvs_c": "c.173+3310G>A",
"hgvs_p": null,
"transcript": "ENST00000532364.1",
"protein_id": "ENSP00000460316.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 103,
"cds_start": -4,
"cds_end": null,
"cds_length": 312,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000297437",
"gene_hgnc_id": null,
"hgvs_c": "n.164+227C>T",
"hgvs_p": null,
"transcript": "ENST00000747910.1",
"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": 352,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VKORC1",
"gene_hgnc_id": 23663,
"dbsnp": "rs777707816",
"frequency_reference_population": 0.000019826199,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000191536,
"gnomad_genomes_af": 0.0000262885,
"gnomad_exomes_ac": 28,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3361828327178955,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.72,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3759,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.725,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_024006.6",
"gene_symbol": "VKORC1",
"hgnc_id": 23663,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.379G>A",
"hgvs_p": "p.Val127Met"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000529564.1",
"gene_symbol": "ENSG00000255439",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.283+2065G>A",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000747910.1",
"gene_symbol": "ENSG00000297437",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.164+227C>T",
"hgvs_p": null
}
],
"clinvar_disease": " combined deficiency of, type 2,Vitamin K-dependent clotting factors",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Vitamin K-dependent clotting factors, combined deficiency of, type 2",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}