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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: 19-5208050-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=5208050&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PP3_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PTPRS",
"hgnc_id": 9681,
"hgvs_c": "c.5650G>A",
"hgvs_p": "p.Val1884Met",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_002850.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_score": -2,
"allele_count_reference_population": 14,
"alphamissense_prediction": null,
"alphamissense_score": 0.8116,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.01,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8534058332443237,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1948,
"aa_ref": "V",
"aa_start": 1884,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7356,
"cdna_start": 5893,
"cds_end": null,
"cds_length": 5847,
"cds_start": 5650,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "NM_002850.4",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5650G>A",
"hgvs_p": "p.Val1884Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000262963.11",
"protein_coding": true,
"protein_id": "NP_002841.3",
"strand": false,
"transcript": "NM_002850.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1948,
"aa_ref": "V",
"aa_start": 1884,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7356,
"cdna_start": 5893,
"cds_end": null,
"cds_length": 5847,
"cds_start": 5650,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "ENST00000262963.11",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5650G>A",
"hgvs_p": "p.Val1884Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002850.4",
"protein_coding": true,
"protein_id": "ENSP00000262963.8",
"strand": false,
"transcript": "ENST00000262963.11",
"transcript_support_level": 5
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1948,
"aa_ref": "V",
"aa_start": 1884,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6353,
"cdna_start": 5750,
"cds_end": null,
"cds_length": 5847,
"cds_start": 5650,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "ENST00000587303.5",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5650G>A",
"hgvs_p": "p.Val1884Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000467537.1",
"strand": false,
"transcript": "ENST00000587303.5",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1910,
"aa_ref": "V",
"aa_start": 1846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5993,
"cdna_start": 5559,
"cds_end": null,
"cds_length": 5733,
"cds_start": 5536,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "ENST00000588012.5",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5536G>A",
"hgvs_p": "p.Val1846Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000465443.1",
"strand": false,
"transcript": "ENST00000588012.5",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1501,
"aa_ref": "V",
"aa_start": 1437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4766,
"cdna_start": 4332,
"cds_end": null,
"cds_length": 4506,
"cds_start": 4309,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000592099.5",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.4309G>A",
"hgvs_p": "p.Val1437Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000467398.1",
"strand": false,
"transcript": "ENST00000592099.5",
"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": 5443,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 31,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000588552.5",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "n.4591G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000588552.5",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1926,
"aa_ref": "V",
"aa_start": 1862,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7290,
"cdna_start": 5827,
"cds_end": null,
"cds_length": 5781,
"cds_start": 5584,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "NM_001394011.1",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5584G>A",
"hgvs_p": "p.Val1862Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001380940.1",
"strand": false,
"transcript": "NM_001394011.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1919,
"aa_ref": "V",
"aa_start": 1855,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7269,
"cdna_start": 5806,
"cds_end": null,
"cds_length": 5760,
"cds_start": 5563,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "NM_001394012.1",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5563G>A",
"hgvs_p": "p.Val1855Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001380941.1",
"strand": false,
"transcript": "NM_001394012.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1910,
"aa_ref": "V",
"aa_start": 1846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7242,
"cdna_start": 5779,
"cds_end": null,
"cds_length": 5733,
"cds_start": 5536,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "NM_130854.3",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5536G>A",
"hgvs_p": "p.Val1846Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_570924.2",
"strand": false,
"transcript": "NM_130854.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1906,
"aa_ref": "V",
"aa_start": 1842,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7230,
"cdna_start": 5767,
"cds_end": null,
"cds_length": 5721,
"cds_start": 5524,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "NM_001394013.1",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5524G>A",
"hgvs_p": "p.Val1842Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001380942.1",
"strand": false,
"transcript": "NM_001394013.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1906,
"aa_ref": "V",
"aa_start": 1842,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7365,
"cdna_start": 5896,
"cds_end": null,
"cds_length": 5721,
"cds_start": 5524,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "ENST00000919618.1",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5524G>A",
"hgvs_p": "p.Val1842Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589677.1",
"strand": false,
"transcript": "ENST00000919618.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1672,
"aa_ref": "V",
"aa_start": 1608,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7297,
"cdna_start": 5241,
"cds_end": null,
"cds_length": 5019,
"cds_start": 4822,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000850941.1",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.4822G>A",
"hgvs_p": "p.Val1608Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521026.1",
"strand": false,
"transcript": "ENST00000850941.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1513,
"aa_ref": "V",
"aa_start": 1449,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6067,
"cdna_start": 4604,
"cds_end": null,
"cds_length": 4542,
"cds_start": 4345,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000919619.1",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.4345G>A",
"hgvs_p": "p.Val1449Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589678.1",
"strand": false,
"transcript": "ENST00000919619.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1505,
"aa_ref": "V",
"aa_start": 1441,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6027,
"cdna_start": 4564,
"cds_end": null,
"cds_length": 4518,
"cds_start": 4321,
"consequences": [
"missense_variant"
],
"exon_count": 30,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "NM_130855.3",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.4321G>A",
"hgvs_p": "p.Val1441Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_570925.2",
"strand": false,
"transcript": "NM_130855.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1501,
"aa_ref": "V",
"aa_start": 1437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6015,
"cdna_start": 4552,
"cds_end": null,
"cds_length": 4506,
"cds_start": 4309,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_130853.3",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.4309G>A",
"hgvs_p": "p.Val1437Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_570923.2",
"strand": false,
"transcript": "NM_130853.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1939,
"aa_ref": "V",
"aa_start": 1875,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7285,
"cdna_start": 5822,
"cds_end": null,
"cds_length": 5820,
"cds_start": 5623,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_017027065.2",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5623G>A",
"hgvs_p": "p.Val1875Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882554.1",
"strand": false,
"transcript": "XM_017027065.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1939,
"aa_ref": "V",
"aa_start": 1875,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7329,
"cdna_start": 5866,
"cds_end": null,
"cds_length": 5820,
"cds_start": 5623,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_017027066.2",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5623G>A",
"hgvs_p": "p.Val1875Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882555.1",
"strand": false,
"transcript": "XM_017027066.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1939,
"aa_ref": "V",
"aa_start": 1875,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7235,
"cdna_start": 5772,
"cds_end": null,
"cds_length": 5820,
"cds_start": 5623,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_017027067.2",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5623G>A",
"hgvs_p": "p.Val1875Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882556.1",
"strand": false,
"transcript": "XM_017027067.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1935,
"aa_ref": "V",
"aa_start": 1871,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7273,
"cdna_start": 5810,
"cds_end": null,
"cds_length": 5808,
"cds_start": 5611,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_005259600.3",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5611G>A",
"hgvs_p": "p.Val1871Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005259657.1",
"strand": false,
"transcript": "XM_005259600.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1935,
"aa_ref": "V",
"aa_start": 1871,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7273,
"cdna_start": 5810,
"cds_end": null,
"cds_length": 5808,
"cds_start": 5611,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_017027068.2",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "c.5611G>A",
"hgvs_p": "p.Val1871Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882557.1",
"strand": false,
"transcript": "XM_017027068.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1935,
"aa_ref": "V",
"aa_start": 1871,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7317,
"cdna_start": 5854,
"cds_end": null,
"cds_length": 5808,
"cds_start": 5611,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_047439155.1",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
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"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
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"feature": "ENST00000706768.1",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "n.960G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000706768.1",
"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": 845,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000706769.1",
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"hgvs_c": "n.*119G>A",
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"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000706769.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs759155627",
"effect": "missense_variant",
"frequency_reference_population": 0.000008686803,
"gene_hgnc_id": 9681,
"gene_symbol": "PTPRS",
"gnomad_exomes_ac": 13,
"gnomad_exomes_af": 0.00000890788,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065678,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.809,
"pos": 5208050,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.76,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002850.4"
}
]
}