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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: 2-241767760-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=241767760&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "D2HGDH",
"hgnc_id": 28358,
"hgvs_c": "c.1357C>T",
"hgvs_p": "p.Leu453Phe",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_152783.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1,BS2",
"acmg_score": -12,
"allele_count_reference_population": 1529,
"alphamissense_prediction": null,
"alphamissense_score": 0.2123,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.31,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "D-2-hydroxyglutaric aciduria 1,D2HGDH-related disorder,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.058692336082458496,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 521,
"aa_ref": "L",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2566,
"cdna_start": 1515,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1357,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_152783.5",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1357C>T",
"hgvs_p": "p.Leu453Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000321264.9",
"protein_coding": true,
"protein_id": "NP_689996.4",
"strand": true,
"transcript": "NM_152783.5",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 521,
"aa_ref": "L",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2566,
"cdna_start": 1515,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1357,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000321264.9",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1357C>T",
"hgvs_p": "p.Leu453Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_152783.5",
"protein_coding": true,
"protein_id": "ENSP00000315351.4",
"strand": true,
"transcript": "ENST00000321264.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4549,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000436747.5",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "n.*2593C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000400212.1",
"strand": true,
"transcript": "ENST00000436747.5",
"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": 2298,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000468064.5",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "n.1247C>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": "ENST00000468064.5",
"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": 1026,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000470343.5",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "n.838C>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": "ENST00000470343.5",
"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": 1612,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000473126.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "n.556C>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": "ENST00000473126.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2232,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000486953.5",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "n.1181C>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": "ENST00000486953.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4549,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000436747.5",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "n.*2593C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000400212.1",
"strand": true,
"transcript": "ENST00000436747.5",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 596,
"aa_ref": "L",
"aa_start": 528,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2795,
"cdna_start": 1740,
"cds_end": null,
"cds_length": 1791,
"cds_start": 1582,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000951632.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1582C>T",
"hgvs_p": "p.Leu528Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621691.1",
"strand": true,
"transcript": "ENST00000951632.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 583,
"aa_ref": "L",
"aa_start": 515,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2759,
"cdna_start": 1708,
"cds_end": null,
"cds_length": 1752,
"cds_start": 1543,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000951631.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1543C>T",
"hgvs_p": "p.Leu515Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621690.1",
"strand": true,
"transcript": "ENST00000951631.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 561,
"aa_ref": "L",
"aa_start": 493,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2665,
"cdna_start": 1614,
"cds_end": null,
"cds_length": 1686,
"cds_start": 1477,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000951636.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1477C>T",
"hgvs_p": "p.Leu493Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621695.1",
"strand": true,
"transcript": "ENST00000951636.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 548,
"aa_ref": "L",
"aa_start": 480,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2644,
"cdna_start": 1595,
"cds_end": null,
"cds_length": 1647,
"cds_start": 1438,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000951634.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1438C>T",
"hgvs_p": "p.Leu480Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621693.1",
"strand": true,
"transcript": "ENST00000951634.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 547,
"aa_ref": "L",
"aa_start": 479,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2677,
"cdna_start": 1621,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1435,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000910513.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1435C>T",
"hgvs_p": "p.Leu479Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580572.1",
"strand": true,
"transcript": "ENST00000910513.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 547,
"aa_ref": "L",
"aa_start": 479,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2804,
"cdna_start": 1756,
"cds_end": null,
"cds_length": 1644,
"cds_start": 1435,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910524.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1435C>T",
"hgvs_p": "p.Leu479Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580583.1",
"strand": true,
"transcript": "ENST00000910524.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 546,
"aa_ref": "L",
"aa_start": 478,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2642,
"cdna_start": 1591,
"cds_end": null,
"cds_length": 1641,
"cds_start": 1432,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000910522.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1432C>T",
"hgvs_p": "p.Leu478Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580581.1",
"strand": true,
"transcript": "ENST00000910522.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 535,
"aa_ref": "L",
"aa_start": 467,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2629,
"cdna_start": 1578,
"cds_end": null,
"cds_length": 1608,
"cds_start": 1399,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000910517.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1399C>T",
"hgvs_p": "p.Leu467Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580576.1",
"strand": true,
"transcript": "ENST00000910517.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 527,
"aa_ref": "L",
"aa_start": 459,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2596,
"cdna_start": 1545,
"cds_end": null,
"cds_length": 1584,
"cds_start": 1375,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910519.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1375C>T",
"hgvs_p": "p.Leu459Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580578.1",
"strand": true,
"transcript": "ENST00000910519.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 521,
"aa_ref": "L",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2595,
"cdna_start": 1539,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1357,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910514.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1357C>T",
"hgvs_p": "p.Leu453Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580573.1",
"strand": true,
"transcript": "ENST00000910514.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 521,
"aa_ref": "L",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3008,
"cdna_start": 1952,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1357,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000910520.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1357C>T",
"hgvs_p": "p.Leu453Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580579.1",
"strand": true,
"transcript": "ENST00000910520.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 520,
"aa_ref": "L",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2589,
"cdna_start": 1533,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910515.1",
"gene_hgnc_id": 28358,
"gene_symbol": "D2HGDH",
"hgvs_c": "c.1354C>T",
"hgvs_p": "p.Leu452Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580574.1",
"strand": true,
"transcript": "ENST00000910515.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 520,
"aa_ref": "L",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2555,
"cdna_start": 1506,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000951635.1",
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