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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: 19-49862259-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49862259&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PNKP",
"hgnc_id": 9154,
"hgvs_c": "c.1052C>T",
"hgvs_p": "p.Pro351Leu",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -1,
"transcript": "NM_007254.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_score": -1,
"allele_count_reference_population": 20,
"alphamissense_prediction": null,
"alphamissense_score": 0.1228,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " 12,Ataxia - oculomotor apraxia type 4,Developmental and epileptic encephalopathy,Inborn genetic diseases,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.31214818358421326,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 521,
"aa_ref": "P",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1731,
"cdna_start": 1173,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1052,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_007254.4",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1052C>T",
"hgvs_p": "p.Pro351Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000322344.8",
"protein_coding": true,
"protein_id": "NP_009185.2",
"strand": false,
"transcript": "NM_007254.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 521,
"aa_ref": "P",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1731,
"cdna_start": 1173,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1052,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000322344.8",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1052C>T",
"hgvs_p": "p.Pro351Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007254.4",
"protein_coding": true,
"protein_id": "ENSP00000323511.2",
"strand": false,
"transcript": "ENST00000322344.8",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 521,
"aa_ref": "P",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1665,
"cdna_start": 1134,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1052,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000596014.5",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1052C>T",
"hgvs_p": "p.Pro351Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000472300.1",
"strand": false,
"transcript": "ENST00000596014.5",
"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": 1723,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000593946.5",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "n.*979C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468896.1",
"strand": false,
"transcript": "ENST00000593946.5",
"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": 1723,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000593946.5",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "n.*979C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468896.1",
"strand": false,
"transcript": "ENST00000593946.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 530,
"aa_ref": "P",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1749,
"cdna_start": 1190,
"cds_end": null,
"cds_length": 1593,
"cds_start": 1079,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000861313.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1079C>T",
"hgvs_p": "p.Pro360Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531372.1",
"strand": false,
"transcript": "ENST00000861313.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 530,
"aa_ref": "P",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1665,
"cdna_start": 1107,
"cds_end": null,
"cds_length": 1593,
"cds_start": 1079,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000934451.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1079C>T",
"hgvs_p": "p.Pro360Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604510.1",
"strand": false,
"transcript": "ENST00000934451.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 521,
"aa_ref": "P",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1859,
"cdna_start": 1303,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1052,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000934445.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1052C>T",
"hgvs_p": "p.Pro351Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604504.1",
"strand": false,
"transcript": "ENST00000934445.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 521,
"aa_ref": "P",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1653,
"cdna_start": 1098,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1052,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000934450.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1052C>T",
"hgvs_p": "p.Pro351Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604509.1",
"strand": false,
"transcript": "ENST00000934450.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 514,
"aa_ref": "P",
"aa_start": 344,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1686,
"cdna_start": 1131,
"cds_end": null,
"cds_length": 1545,
"cds_start": 1031,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000934449.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1031C>T",
"hgvs_p": "p.Pro344Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604508.1",
"strand": false,
"transcript": "ENST00000934449.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 510,
"aa_ref": "P",
"aa_start": 340,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1655,
"cdna_start": 1101,
"cds_end": null,
"cds_length": 1533,
"cds_start": 1019,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000965095.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Pro340Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635154.1",
"strand": false,
"transcript": "ENST00000965095.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 508,
"aa_ref": "P",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1674,
"cdna_start": 1119,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1013,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000934448.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1013C>T",
"hgvs_p": "p.Pro338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604507.1",
"strand": false,
"transcript": "ENST00000934448.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 507,
"aa_ref": "P",
"aa_start": 337,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1686,
"cdna_start": 1130,
"cds_end": null,
"cds_length": 1524,
"cds_start": 1010,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000861311.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1010C>T",
"hgvs_p": "p.Pro337Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531370.1",
"strand": false,
"transcript": "ENST00000861311.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 490,
"aa_ref": "P",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1602,
"cdna_start": 1080,
"cds_end": null,
"cds_length": 1473,
"cds_start": 959,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000600573.5",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.959C>T",
"hgvs_p": "p.Pro320Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000469826.1",
"strand": false,
"transcript": "ENST00000600573.5",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 485,
"aa_ref": "P",
"aa_start": 315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1545,
"cdna_start": 998,
"cds_end": null,
"cds_length": 1458,
"cds_start": 944,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000631020.2",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.944C>T",
"hgvs_p": "p.Pro315Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000486707.1",
"strand": false,
"transcript": "ENST00000631020.2",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 479,
"aa_ref": "P",
"aa_start": 309,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1602,
"cdna_start": 1044,
"cds_end": null,
"cds_length": 1440,
"cds_start": 926,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000861312.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.926C>T",
"hgvs_p": "p.Pro309Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531371.1",
"strand": false,
"transcript": "ENST00000861312.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 479,
"aa_ref": "P",
"aa_start": 309,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1544,
"cdna_start": 987,
"cds_end": null,
"cds_length": 1440,
"cds_start": 926,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000965096.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.926C>T",
"hgvs_p": "p.Pro309Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635155.1",
"strand": false,
"transcript": "ENST00000965096.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 472,
"aa_ref": "P",
"aa_start": 302,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1568,
"cdna_start": 1011,
"cds_end": null,
"cds_length": 1419,
"cds_start": 905,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000965094.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.905C>T",
"hgvs_p": "p.Pro302Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635153.1",
"strand": false,
"transcript": "ENST00000965094.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 471,
"aa_ref": "P",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1581,
"cdna_start": 1173,
"cds_end": null,
"cds_length": 1416,
"cds_start": 1052,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000934444.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1052C>T",
"hgvs_p": "p.Pro351Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604503.1",
"strand": false,
"transcript": "ENST00000934444.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 455,
"aa_ref": "P",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1600,
"cdna_start": 1152,
"cds_end": null,
"cds_length": 1368,
"cds_start": 1052,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000600910.5",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
"hgvs_c": "c.1052C>T",
"hgvs_p": "p.Pro351Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000473137.1",
"strand": false,
"transcript": "ENST00000600910.5",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 455,
"aa_ref": "P",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1517,
"cdna_start": 1157,
"cds_end": null,
"cds_length": 1368,
"cds_start": 1052,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000934447.1",
"gene_hgnc_id": 9154,
"gene_symbol": "PNKP",
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