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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: 16-681446-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=681446&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "STUB1",
"hgnc_id": 11427,
"hgvs_c": "c.367C>A",
"hgvs_p": "p.Leu123Met",
"inheritance_mode": "AD,AR",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_005861.4",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"downstream_gene_variant"
],
"gene_symbol": "JMJD8",
"hgnc_id": 14148,
"hgvs_c": "c.*1348G>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_001005920.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2",
"acmg_score": 7,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.3345,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.1,
"chr": "16",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.7430974841117859,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 303,
"aa_ref": "L",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1340,
"cdna_start": 483,
"cds_end": null,
"cds_length": 912,
"cds_start": 367,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_005861.4",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.367C>A",
"hgvs_p": "p.Leu123Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000219548.9",
"protein_coding": true,
"protein_id": "NP_005852.2",
"strand": true,
"transcript": "NM_005861.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 303,
"aa_ref": "L",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1340,
"cdna_start": 483,
"cds_end": null,
"cds_length": 912,
"cds_start": 367,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000219548.9",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.367C>A",
"hgvs_p": "p.Leu123Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005861.4",
"protein_coding": true,
"protein_id": "ENSP00000219548.4",
"strand": true,
"transcript": "ENST00000219548.9",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 231,
"aa_ref": "L",
"aa_start": 51,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1560,
"cdna_start": 758,
"cds_end": null,
"cds_length": 696,
"cds_start": 151,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000565677.5",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.151C>A",
"hgvs_p": "p.Leu51Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000457228.1",
"strand": true,
"transcript": "ENST00000565677.5",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 336,
"aa_ref": "L",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1408,
"cdna_start": 485,
"cds_end": null,
"cds_length": 1011,
"cds_start": 367,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000965393.1",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.367C>A",
"hgvs_p": "p.Leu123Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635452.1",
"strand": true,
"transcript": "ENST00000965393.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 314,
"aa_ref": "L",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1330,
"cdna_start": 495,
"cds_end": null,
"cds_length": 945,
"cds_start": 367,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000880078.1",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.367C>A",
"hgvs_p": "p.Leu123Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550137.1",
"strand": true,
"transcript": "ENST00000880078.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 312,
"aa_ref": "L",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1313,
"cdna_start": 486,
"cds_end": null,
"cds_length": 939,
"cds_start": 367,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000880079.1",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.367C>A",
"hgvs_p": "p.Leu123Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550138.1",
"strand": true,
"transcript": "ENST00000880079.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 302,
"aa_ref": "L",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1767,
"cdna_start": 913,
"cds_end": null,
"cds_length": 909,
"cds_start": 367,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000880076.1",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.367C>A",
"hgvs_p": "p.Leu123Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550135.1",
"strand": true,
"transcript": "ENST00000880076.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 254,
"aa_ref": "L",
"aa_start": 74,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1496,
"cdna_start": 638,
"cds_end": null,
"cds_length": 765,
"cds_start": 220,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000880077.1",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.220C>A",
"hgvs_p": "p.Leu74Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550136.1",
"strand": true,
"transcript": "ENST00000880077.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 231,
"aa_ref": "L",
"aa_start": 51,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1429,
"cdna_start": 572,
"cds_end": null,
"cds_length": 696,
"cds_start": 151,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001293197.2",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.151C>A",
"hgvs_p": "p.Leu51Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001280126.1",
"strand": true,
"transcript": "NM_001293197.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 231,
"aa_ref": "L",
"aa_start": 51,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 875,
"cdna_start": 323,
"cds_end": null,
"cds_length": 696,
"cds_start": 151,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000564370.5",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.151C>A",
"hgvs_p": "p.Leu51Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000456875.1",
"strand": true,
"transcript": "ENST00000564370.5",
"transcript_support_level": 2
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 212,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 743,
"cdna_start": 412,
"cds_end": null,
"cds_length": 641,
"cds_start": 310,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000567173.5",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.310C>A",
"hgvs_p": "p.Leu104Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000456591.1",
"strand": true,
"transcript": "ENST00000567173.5",
"transcript_support_level": 3
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 184,
"aa_ref": "L",
"aa_start": 28,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 684,
"cdna_start": 84,
"cds_end": null,
"cds_length": 555,
"cds_start": 82,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000566408.5",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.82C>A",
"hgvs_p": "p.Leu28Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000457583.1",
"strand": true,
"transcript": "ENST00000566408.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 152,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 854,
"cdna_start": null,
"cds_end": null,
"cds_length": 459,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000917532.1",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.160-574C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587591.1",
"strand": true,
"transcript": "ENST00000917532.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 894,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000563505.5",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "n.463C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000563505.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 510,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000566181.2",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "n.136C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000566181.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1853,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000569248.5",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "n.941C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000569248.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 264,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1934,
"cdna_start": null,
"cds_end": null,
"cds_length": 795,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001005920.4",
"gene_hgnc_id": 14148,
"gene_symbol": "JMJD8",
"hgvs_c": "c.*1348G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000609261.6",
"protein_coding": true,
"protein_id": "NP_001005920.3",
"strand": true,
"transcript": "NM_001005920.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 264,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1934,
"cdna_start": null,
"cds_end": null,
"cds_length": 795,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000609261.6",
"gene_hgnc_id": 14148,
"gene_symbol": "JMJD8",
"hgvs_c": "c.*1348G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001005920.4",
"protein_coding": true,
"protein_id": "ENSP00000477481.1",
"strand": true,
"transcript": "ENST00000609261.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2205,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000567120.5",
"gene_hgnc_id": 14148,
"gene_symbol": "JMJD8",
"hgvs_c": "n.*225G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000567120.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 156,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 729,
"cdna_start": null,
"cds_end": null,
"cds_length": 471,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000564316.1",
"gene_hgnc_id": 11427,
"gene_symbol": "STUB1",
"hgvs_c": "c.-36C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000457090.1",
"strand": true,
"transcript": "ENST00000564316.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 270,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1948,
"cdna_start": null,
"cds_end": null,
"cds_length": 813,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 9,
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