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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: 1-113852059-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=113852059&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "PTPN22",
"hgnc_id": 9652,
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"inheritance_mode": "Unknown,AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_015967.8",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "AP4B1-AS1",
"hgnc_id": 44114,
"hgvs_c": "n.414+36587G>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "NR_125965.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 16,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.35,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.3499999940395355,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 807,
"aa_ref": "R",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3607,
"cdna_start": 885,
"cds_end": null,
"cds_length": 2424,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_015967.8",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000359785.10",
"protein_coding": true,
"protein_id": "NP_057051.4",
"strand": false,
"transcript": "NM_015967.8",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 807,
"aa_ref": "R",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3607,
"cdna_start": 885,
"cds_end": null,
"cds_length": 2424,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000359785.10",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015967.8",
"protein_coding": true,
"protein_id": "ENSP00000352833.5",
"strand": false,
"transcript": "ENST00000359785.10",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 795,
"aa_ref": "R",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2726,
"cdna_start": 885,
"cds_end": null,
"cds_length": 2388,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000420377.6",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000388229.2",
"strand": false,
"transcript": "ENST00000420377.6",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 783,
"aa_ref": "R",
"aa_start": 242,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3575,
"cdna_start": 854,
"cds_end": null,
"cds_length": 2352,
"cds_start": 724,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000538253.5",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.724C>A",
"hgvs_p": "p.Arg242Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000439372.2",
"strand": false,
"transcript": "ENST00000538253.5",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 668,
"aa_ref": "R",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2118,
"cdna_start": 504,
"cds_end": null,
"cds_length": 2007,
"cds_start": 415,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000525799.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.415C>A",
"hgvs_p": "p.Arg139Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000432674.1",
"strand": false,
"transcript": "ENST00000525799.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 752,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3424,
"cdna_start": null,
"cds_end": null,
"cds_length": 2259,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000528414.5",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.750+2412C>A",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000435176.1",
"strand": false,
"transcript": "ENST00000528414.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 179,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1794,
"cdna_start": null,
"cds_end": null,
"cds_length": 540,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000460620.5",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.468+4323C>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000433141.1",
"strand": false,
"transcript": "ENST00000460620.5",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 832,
"aa_ref": "R",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3712,
"cdna_start": 918,
"cds_end": null,
"cds_length": 2499,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910047.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580106.1",
"strand": false,
"transcript": "ENST00000910047.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 806,
"aa_ref": "R",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3598,
"cdna_start": 882,
"cds_end": null,
"cds_length": 2421,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000941803.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611862.1",
"strand": false,
"transcript": "ENST00000941803.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 800,
"aa_ref": "R",
"aa_start": 259,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3566,
"cdna_start": 853,
"cds_end": null,
"cds_length": 2403,
"cds_start": 775,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910051.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.775C>A",
"hgvs_p": "p.Arg259Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580110.1",
"strand": false,
"transcript": "ENST00000910051.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 794,
"aa_ref": "R",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3210,
"cdna_start": 885,
"cds_end": null,
"cds_length": 2385,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910052.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580111.1",
"strand": false,
"transcript": "ENST00000910052.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 783,
"aa_ref": "R",
"aa_start": 242,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3535,
"cdna_start": 813,
"cds_end": null,
"cds_length": 2352,
"cds_start": 724,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001308297.2",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.724C>A",
"hgvs_p": "p.Arg242Arg",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001295226.2",
"strand": false,
"transcript": "NM_001308297.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
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"aa_length": 779,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3523,
"cdna_start": 885,
"cds_end": null,
"cds_length": 2340,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001193431.3",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001180360.2",
"strand": false,
"transcript": "NM_001193431.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 779,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3554,
"cdna_start": 916,
"cds_end": null,
"cds_length": 2340,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910046.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580105.1",
"strand": false,
"transcript": "ENST00000910046.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 778,
"aa_ref": "R",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3518,
"cdna_start": 885,
"cds_end": null,
"cds_length": 2337,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910048.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580107.1",
"strand": false,
"transcript": "ENST00000910048.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 755,
"aa_ref": "R",
"aa_start": 242,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3445,
"cdna_start": 810,
"cds_end": null,
"cds_length": 2268,
"cds_start": 724,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000910050.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.724C>A",
"hgvs_p": "p.Arg242Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580109.1",
"strand": false,
"transcript": "ENST00000910050.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
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"aa_length": 737,
"aa_ref": "R",
"aa_start": 196,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2735,
"cdna_start": 699,
"cds_end": null,
"cds_length": 2214,
"cds_start": 586,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000910053.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.586C>A",
"hgvs_p": "p.Arg196Arg",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580112.1",
"strand": false,
"transcript": "ENST00000910053.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
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"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3623,
"cdna_start": 932,
"cds_end": null,
"cds_length": 2322,
"cds_start": 796,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011541222.2",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Arg266Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539524.1",
"strand": false,
"transcript": "XM_011541222.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
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"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3498,
"cdna_start": 860,
"cds_end": null,
"cds_length": 2268,
"cds_start": 724,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047417631.1",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.724C>A",
"hgvs_p": "p.Arg242Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047273587.1",
"strand": false,
"transcript": "XM_047417631.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 749,
"aa_ref": "R",
"aa_start": 242,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3551,
"cdna_start": 860,
"cds_end": null,
"cds_length": 2250,
"cds_start": 724,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011541225.3",
"gene_hgnc_id": 9652,
"gene_symbol": "PTPN22",
"hgvs_c": "c.724C>A",
"hgvs_p": "p.Arg242Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539527.1",
"strand": false,
"transcript": "XM_011541225.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 715,
"aa_ref": "R",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3815,
"cdna_start": 932,
"cds_end": null,
"cds_length": 2148,
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