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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: 5-115841522-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=115841522&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 115841522,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004707.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "c.31C>G",
"hgvs_p": "p.Leu11Val",
"transcript": "NM_004707.4",
"protein_id": "NP_004698.3",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 140,
"cds_start": 31,
"cds_end": null,
"cds_length": 423,
"cdna_start": 44,
"cdna_end": null,
"cdna_length": 4040,
"mane_select": "ENST00000509910.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004707.4"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "c.31C>G",
"hgvs_p": "p.Leu11Val",
"transcript": "ENST00000509910.2",
"protein_id": "ENSP00000425107.1",
"transcript_support_level": 1,
"aa_start": 11,
"aa_end": null,
"aa_length": 140,
"cds_start": 31,
"cds_end": null,
"cds_length": 423,
"cdna_start": 44,
"cdna_end": null,
"cdna_length": 4040,
"mane_select": "NM_004707.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000509910.2"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "c.31C>G",
"hgvs_p": "p.Leu11Val",
"transcript": "ENST00000500945.2",
"protein_id": "ENSP00000425164.1",
"transcript_support_level": 1,
"aa_start": 11,
"aa_end": null,
"aa_length": 74,
"cds_start": 31,
"cds_end": null,
"cds_length": 225,
"cdna_start": 44,
"cdna_end": null,
"cdna_length": 1430,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000500945.2"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "c.31C>G",
"hgvs_p": "p.Leu11Val",
"transcript": "ENST00000914944.1",
"protein_id": "ENSP00000585003.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 119,
"cds_start": 31,
"cds_end": null,
"cds_length": 360,
"cdna_start": 44,
"cdna_end": null,
"cdna_length": 698,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914944.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "c.31C>G",
"hgvs_p": "p.Leu11Val",
"transcript": "NM_001277783.2",
"protein_id": "NP_001264712.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 74,
"cds_start": 31,
"cds_end": null,
"cds_length": 225,
"cdna_start": 44,
"cdna_end": null,
"cdna_length": 3903,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001277783.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3S1",
"gene_hgnc_id": 2013,
"hgvs_c": "c.-516G>C",
"hgvs_p": null,
"transcript": "ENST00000905986.1",
"protein_id": "ENSP00000576045.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 125,
"cds_start": null,
"cds_end": null,
"cds_length": 378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1589,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905986.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "n.31C>G",
"hgvs_p": null,
"transcript": "ENST00000379594.7",
"protein_id": "ENSP00000368913.3",
"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": 1082,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000379594.7"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "n.43C>G",
"hgvs_p": null,
"transcript": "ENST00000505993.5",
"protein_id": "ENSP00000425948.1",
"transcript_support_level": 3,
"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": 773,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000505993.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "n.22C>G",
"hgvs_p": null,
"transcript": "ENST00000513167.1",
"protein_id": "ENSP00000425277.1",
"transcript_support_level": 3,
"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": 732,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000513167.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "n.31C>G",
"hgvs_p": null,
"transcript": "ENST00000513322.5",
"protein_id": "ENSP00000424529.1",
"transcript_support_level": 3,
"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": 1558,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000513322.5"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "n.38C>G",
"hgvs_p": null,
"transcript": "ENST00000514775.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 553,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000514775.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "n.44C>G",
"hgvs_p": null,
"transcript": "NR_033362.2",
"protein_id": null,
"transcript_support_level": null,
"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": 4157,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033362.2"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "n.44C>G",
"hgvs_p": null,
"transcript": "NR_033363.2",
"protein_id": null,
"transcript_support_level": null,
"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": 4156,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033363.2"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"hgvs_c": "n.44C>G",
"hgvs_p": null,
"transcript": "NR_073603.2",
"protein_id": null,
"transcript_support_level": null,
"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": 4273,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_073603.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3S1",
"gene_hgnc_id": 2013,
"hgvs_c": "c.-516G>C",
"hgvs_p": null,
"transcript": "ENST00000905987.1",
"protein_id": "ENSP00000576046.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": null,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1596,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905987.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3S1",
"gene_hgnc_id": 2013,
"hgvs_c": "n.-70G>C",
"hgvs_p": null,
"transcript": "ENST00000514118.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 392,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000514118.5"
}
],
"gene_symbol": "ATG12",
"gene_hgnc_id": 588,
"dbsnp": "rs561016735",
"frequency_reference_population": 0.00000558071,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000479278,
"gnomad_genomes_af": 0.0000131434,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10036864876747131,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.044,
"revel_prediction": "Benign",
"alphamissense_score": 0.0704,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.479,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_004707.4",
"gene_symbol": "ATG12",
"hgnc_id": 588,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.31C>G",
"hgvs_p": "p.Leu11Val"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000905986.1",
"gene_symbol": "AP3S1",
"hgnc_id": 2013,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-516G>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}