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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: 6-113959978-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=113959978&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 113959978,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000519065.6",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.93G>A",
"hgvs_p": "p.Met31Ile",
"transcript": "NM_001527.4",
"protein_id": "NP_001518.3",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 488,
"cds_start": 93,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 333,
"cdna_end": null,
"cdna_length": 9737,
"mane_select": "ENST00000519065.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.93G>A",
"hgvs_p": "p.Met31Ile",
"transcript": "ENST00000519065.6",
"protein_id": "ENSP00000430432.1",
"transcript_support_level": 1,
"aa_start": 31,
"aa_end": null,
"aa_length": 488,
"cds_start": 93,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 333,
"cdna_end": null,
"cdna_length": 9737,
"mane_select": "NM_001527.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000368632.6",
"protein_id": "ENSP00000357621.2",
"transcript_support_level": 2,
"aa_start": 1,
"aa_end": null,
"aa_length": 458,
"cds_start": 3,
"cds_end": null,
"cds_length": 1377,
"cdna_start": 370,
"cdna_end": null,
"cdna_length": 2084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000519108.5",
"protein_id": "ENSP00000430008.1",
"transcript_support_level": 2,
"aa_start": 1,
"aa_end": null,
"aa_length": 458,
"cds_start": 3,
"cds_end": null,
"cds_length": 1377,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 2000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000523628.5",
"protein_id": "ENSP00000427861.1",
"transcript_support_level": 4,
"aa_start": 1,
"aa_end": null,
"aa_length": 102,
"cds_start": 3,
"cds_end": null,
"cds_length": 310,
"cdna_start": 242,
"cdna_end": null,
"cdna_length": 549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000521610.5",
"protein_id": "ENSP00000429901.1",
"transcript_support_level": 4,
"aa_start": 1,
"aa_end": null,
"aa_length": 99,
"cds_start": 3,
"cds_end": null,
"cds_length": 301,
"cdna_start": 282,
"cdna_end": null,
"cdna_length": 580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000522371.5",
"protein_id": "ENSP00000428599.1",
"transcript_support_level": 4,
"aa_start": 1,
"aa_end": null,
"aa_length": 85,
"cds_start": 3,
"cds_end": null,
"cds_length": 258,
"cdna_start": 247,
"cdna_end": null,
"cdna_length": 502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000518690.5",
"protein_id": "ENSP00000428653.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 70,
"cds_start": 3,
"cds_end": null,
"cds_length": 213,
"cdna_start": 354,
"cdna_end": null,
"cdna_length": 564,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000523240.5",
"protein_id": "ENSP00000429236.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 64,
"cds_start": 3,
"cds_end": null,
"cds_length": 197,
"cdna_start": 363,
"cdna_end": null,
"cdna_length": 557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000520895.5",
"protein_id": "ENSP00000428861.1",
"transcript_support_level": 4,
"aa_start": 1,
"aa_end": null,
"aa_length": 59,
"cds_start": 3,
"cds_end": null,
"cds_length": 180,
"cdna_start": 374,
"cdna_end": null,
"cdna_length": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000524334.1",
"protein_id": "ENSP00000428989.1",
"transcript_support_level": 4,
"aa_start": 1,
"aa_end": null,
"aa_length": 51,
"cds_start": 3,
"cds_end": null,
"cds_length": 158,
"cdna_start": 415,
"cdna_end": null,
"cdna_length": 570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "XM_047418692.1",
"protein_id": "XP_047274648.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 458,
"cds_start": 3,
"cds_end": null,
"cds_length": 1377,
"cdna_start": 67,
"cdna_end": null,
"cdna_length": 9471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Met21Ile",
"transcript": "ENST00000425835.6",
"protein_id": "ENSP00000417026.2",
"transcript_support_level": 2,
"aa_start": 21,
"aa_end": null,
"aa_length": 161,
"cds_start": 63,
"cds_end": null,
"cds_length": 486,
"cdna_start": 63,
"cdna_end": null,
"cdna_length": 553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "c.114G>A",
"hgvs_p": "p.Met38Ile",
"transcript": "ENST00000521163.5",
"protein_id": "ENSP00000428024.1",
"transcript_support_level": 5,
"aa_start": 38,
"aa_end": null,
"aa_length": 108,
"cds_start": 114,
"cds_end": null,
"cds_length": 328,
"cdna_start": 343,
"cdna_end": null,
"cdna_length": 557,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "n.322G>A",
"hgvs_p": null,
"transcript": "ENST00000520170.1",
"protein_id": null,
"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": 690,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "n.321G>A",
"hgvs_p": null,
"transcript": "ENST00000521233.1",
"protein_id": null,
"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": 733,
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "n.361G>A",
"hgvs_p": null,
"transcript": "NR_033441.2",
"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": 9765,
"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": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"hgvs_c": "n.291G>A",
"hgvs_p": null,
"transcript": "NR_073443.2",
"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": 9695,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HDAC2",
"gene_hgnc_id": 4853,
"dbsnp": "rs1554198179",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9675914645195007,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.595,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9997,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"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_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000519065.6",
"gene_symbol": "HDAC2",
"hgnc_id": 4853,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.93G>A",
"hgvs_p": "p.Met31Ile"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}