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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: 12-112488445-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=112488445&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "PTPN11",
"hgnc_id": 9644,
"hgvs_c": "c.1394C>G",
"hgvs_p": "p.Ala465Gly",
"inheritance_mode": "AD",
"pathogenic_score": 16,
"score": 16,
"transcript": "NM_001330437.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PM5,PP2,PP3_Strong,PP5",
"acmg_score": 16,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9966,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.34,
"chr": "12",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "LEOPARD syndrome 1,PTPN11-related disorder,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9823452234268188,
"computational_source_selected": "CardioboostCm",
"consequences": [
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 593,
"aa_ref": "A",
"aa_start": 461,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6073,
"cdna_start": 1547,
"cds_end": null,
"cds_length": 1782,
"cds_start": 1382,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_002834.5",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1382C>G",
"hgvs_p": "p.Ala461Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000351677.7",
"protein_coding": true,
"protein_id": "NP_002825.3",
"strand": true,
"transcript": "NM_002834.5",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 593,
"aa_ref": "A",
"aa_start": 461,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6073,
"cdna_start": 1547,
"cds_end": null,
"cds_length": 1782,
"cds_start": 1382,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000351677.7",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1382C>G",
"hgvs_p": "p.Ala461Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002834.5",
"protein_coding": true,
"protein_id": "ENSP00000340944.3",
"strand": true,
"transcript": "ENST00000351677.7",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 597,
"aa_ref": "A",
"aa_start": 465,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1794,
"cdna_start": 1394,
"cds_end": null,
"cds_length": 1794,
"cds_start": 1394,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000635625.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1394C>G",
"hgvs_p": "p.Ala465Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489597.1",
"strand": true,
"transcript": "ENST00000635625.1",
"transcript_support_level": 5
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 195,
"aa_ref": "A",
"aa_start": 132,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 588,
"cdna_start": 395,
"cds_end": null,
"cds_length": 588,
"cds_start": 395,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000635652.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.395C>G",
"hgvs_p": "p.Ala132Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489541.1",
"strand": true,
"transcript": "ENST00000635652.1",
"transcript_support_level": 3
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 671,
"aa_ref": "A",
"aa_start": 461,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6274,
"cdna_start": 1587,
"cds_end": null,
"cds_length": 2016,
"cds_start": 1382,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000690210.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1382C>G",
"hgvs_p": "p.Ala461Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509272.1",
"strand": true,
"transcript": "ENST00000690210.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 597,
"aa_ref": "A",
"aa_start": 465,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6085,
"cdna_start": 1559,
"cds_end": null,
"cds_length": 1794,
"cds_start": 1394,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001330437.2",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1394C>G",
"hgvs_p": "p.Ala465Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317366.1",
"strand": true,
"transcript": "NM_001330437.2",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 596,
"aa_ref": "A",
"aa_start": 464,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6120,
"cdna_start": 1602,
"cds_end": null,
"cds_length": 1791,
"cds_start": 1391,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000882517.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1391C>G",
"hgvs_p": "p.Ala464Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000552576.1",
"strand": true,
"transcript": "ENST00000882517.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 592,
"aa_ref": "A",
"aa_start": 460,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6070,
"cdna_start": 1544,
"cds_end": null,
"cds_length": 1779,
"cds_start": 1379,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001374625.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1379C>G",
"hgvs_p": "p.Ala460Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001361554.1",
"strand": true,
"transcript": "NM_001374625.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 592,
"aa_ref": "A",
"aa_start": 460,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6129,
"cdna_start": 1608,
"cds_end": null,
"cds_length": 1779,
"cds_start": 1379,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000882515.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1379C>G",
"hgvs_p": "p.Ala460Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000552574.1",
"strand": true,
"transcript": "ENST00000882515.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 578,
"aa_ref": "A",
"aa_start": 461,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4455,
"cdna_start": 1587,
"cds_end": null,
"cds_length": 1737,
"cds_start": 1382,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000639857.2",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1382C>G",
"hgvs_p": "p.Ala461Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000491593.2",
"strand": true,
"transcript": "ENST00000639857.2",
"transcript_support_level": 5
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 559,
"aa_ref": "A",
"aa_start": 427,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6020,
"cdna_start": 1497,
"cds_end": null,
"cds_length": 1680,
"cds_start": 1280,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000882516.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1280C>G",
"hgvs_p": "p.Ala427Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000552575.1",
"strand": true,
"transcript": "ENST00000882516.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 556,
"aa_ref": "A",
"aa_start": 424,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6000,
"cdna_start": 1479,
"cds_end": null,
"cds_length": 1671,
"cds_start": 1271,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000914890.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1271C>G",
"hgvs_p": "p.Ala424Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584949.1",
"strand": true,
"transcript": "ENST00000914890.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 555,
"aa_ref": "A",
"aa_start": 423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5995,
"cdna_start": 1469,
"cds_end": null,
"cds_length": 1668,
"cds_start": 1268,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000687906.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1268C>G",
"hgvs_p": "p.Ala423Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509536.1",
"strand": true,
"transcript": "ENST00000687906.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 554,
"aa_ref": "A",
"aa_start": 422,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5996,
"cdna_start": 1472,
"cds_end": null,
"cds_length": 1665,
"cds_start": 1265,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000971611.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1265C>G",
"hgvs_p": "p.Ala422Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641670.1",
"strand": true,
"transcript": "ENST00000971611.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 552,
"aa_ref": "A",
"aa_start": 420,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5940,
"cdna_start": 1424,
"cds_end": null,
"cds_length": 1659,
"cds_start": 1259,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000882518.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1259C>G",
"hgvs_p": "p.Ala420Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000552577.1",
"strand": true,
"transcript": "ENST00000882518.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 487,
"aa_ref": "A",
"aa_start": 355,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5759,
"cdna_start": 1244,
"cds_end": null,
"cds_length": 1464,
"cds_start": 1064,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000971614.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1064C>G",
"hgvs_p": "p.Ala355Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641673.1",
"strand": true,
"transcript": "ENST00000971614.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 343,
"aa_ref": "A",
"aa_start": 211,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5356,
"cdna_start": 838,
"cds_end": null,
"cds_length": 1032,
"cds_start": 632,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000971612.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.632C>G",
"hgvs_p": "p.Ala211Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641671.1",
"strand": true,
"transcript": "ENST00000971612.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 329,
"aa_ref": "A",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5307,
"cdna_start": 790,
"cds_end": null,
"cds_length": 990,
"cds_start": 590,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000971613.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.590C>G",
"hgvs_p": "p.Ala197Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641672.1",
"strand": true,
"transcript": "ENST00000971613.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 596,
"aa_ref": "A",
"aa_start": 464,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6082,
"cdna_start": 1556,
"cds_end": null,
"cds_length": 1791,
"cds_start": 1391,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011538613.3",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1391C>G",
"hgvs_p": "p.Ala464Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011536915.1",
"strand": true,
"transcript": "XM_011538613.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 468,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5738,
"cdna_start": null,
"cds_end": null,
"cds_length": 1407,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000688597.1",
"gene_hgnc_id": 9644,
"gene_symbol": "PTPN11",
"hgvs_c": "c.1224+6240C>G",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510628.1",
"strand": true,
"transcript": "ENST00000688597.1",
"transcript_support_level": null
},
{
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}