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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: 1-119735362-AG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=119735362&ref=AG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "PHGDH",
"hgnc_id": 8923,
"hgvs_c": "c.714delG",
"hgvs_p": "p.Ile239fs",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_006623.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_score": 12,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "1",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "PHGDH deficiency",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 533,
"aa_ref": "G",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1866,
"cdna_start": 803,
"cds_end": null,
"cds_length": 1602,
"cds_start": 714,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_006623.4",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.714delG",
"hgvs_p": "p.Ile239fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000641023.2",
"protein_coding": true,
"protein_id": "NP_006614.2",
"strand": true,
"transcript": "NM_006623.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 533,
"aa_ref": "G",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1866,
"cdna_start": 803,
"cds_end": null,
"cds_length": 1602,
"cds_start": 714,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000641023.2",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.714delG",
"hgvs_p": "p.Ile239fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006623.4",
"protein_coding": true,
"protein_id": "ENSP00000493175.1",
"strand": true,
"transcript": "ENST00000641023.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 532,
"aa_ref": "G",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1882,
"cdna_start": 803,
"cds_end": null,
"cds_length": 1599,
"cds_start": 714,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000369409.9",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.714delG",
"hgvs_p": "p.Ile239fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000358417.5",
"strand": true,
"transcript": "ENST00000369409.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 533,
"aa_ref": "G",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2585,
"cdna_start": 1547,
"cds_end": null,
"cds_length": 1602,
"cds_start": 714,
"consequences": [
"frameshift_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000641597.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.714delG",
"hgvs_p": "p.Ile239fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493382.1",
"strand": true,
"transcript": "ENST00000641597.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 526,
"aa_ref": "G",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1774,
"cdna_start": 853,
"cds_end": null,
"cds_length": 1581,
"cds_start": 714,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000641947.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.714delG",
"hgvs_p": "p.Ile239fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492994.1",
"strand": true,
"transcript": "ENST00000641947.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 521,
"aa_ref": "G",
"aa_start": 226,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1828,
"cdna_start": 765,
"cds_end": null,
"cds_length": 1566,
"cds_start": 678,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000858460.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.678delG",
"hgvs_p": "p.Ile227fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528519.1",
"strand": true,
"transcript": "ENST00000858460.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 445,
"aa_ref": "G",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1638,
"cdna_start": 839,
"cds_end": null,
"cds_length": 1338,
"cds_start": 714,
"consequences": [
"frameshift_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000641115.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.714delG",
"hgvs_p": "p.Ile239fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493264.1",
"strand": true,
"transcript": "ENST00000641115.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 442,
"aa_ref": "G",
"aa_start": 147,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1591,
"cdna_start": 526,
"cds_end": null,
"cds_length": 1329,
"cds_start": 441,
"consequences": [
"frameshift_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000936419.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.441delG",
"hgvs_p": "p.Ile148fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606478.1",
"strand": true,
"transcript": "ENST00000936419.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 429,
"aa_ref": "G",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1780,
"cdna_start": 851,
"cds_end": null,
"cds_length": 1290,
"cds_start": 714,
"consequences": [
"frameshift_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000641074.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.714delG",
"hgvs_p": "p.Ile239fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493446.1",
"strand": true,
"transcript": "ENST00000641074.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 409,
"aa_ref": "G",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1504,
"cdna_start": 429,
"cds_end": null,
"cds_length": 1230,
"cds_start": 342,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000936417.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.342delG",
"hgvs_p": "p.Ile115fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606476.1",
"strand": true,
"transcript": "ENST00000936417.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 275,
"aa_ref": "G",
"aa_start": 156,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1031,
"cdna_start": 470,
"cds_end": null,
"cds_length": 828,
"cds_start": 468,
"consequences": [
"frameshift_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000641811.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.468delG",
"hgvs_p": "p.Ile157fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493296.1",
"strand": true,
"transcript": "ENST00000641811.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 238,
"aa_ref": "G",
"aa_start": 216,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 758,
"cdna_start": 688,
"cds_end": null,
"cds_length": 718,
"cds_start": 648,
"consequences": [
"frameshift_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000641272.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.648delG",
"hgvs_p": "p.Ile217fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493432.1",
"strand": true,
"transcript": "ENST00000641272.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 607,
"aa_ref": "G",
"aa_start": 312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2088,
"cdna_start": 1025,
"cds_end": null,
"cds_length": 1824,
"cds_start": 936,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011541226.3",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.936delG",
"hgvs_p": "p.Ile313fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539528.1",
"strand": true,
"transcript": "XM_011541226.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 581,
"aa_ref": "G",
"aa_start": 286,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1989,
"cdna_start": 926,
"cds_end": null,
"cds_length": 1746,
"cds_start": 858,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011541227.3",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.858delG",
"hgvs_p": "p.Ile287fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539529.1",
"strand": true,
"transcript": "XM_011541227.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 570,
"aa_ref": "G",
"aa_start": 275,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1903,
"cdna_start": 840,
"cds_end": null,
"cds_length": 1713,
"cds_start": 825,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011541228.3",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.825delG",
"hgvs_p": "p.Ile276fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539530.1",
"strand": true,
"transcript": "XM_011541228.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 512,
"aa_ref": "G",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2410,
"cdna_start": 1347,
"cds_end": null,
"cds_length": 1539,
"cds_start": 651,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047417680.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.651delG",
"hgvs_p": "p.Ile218fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047273636.1",
"strand": true,
"transcript": "XM_047417680.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 438,
"aa_ref": "G",
"aa_start": 143,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2176,
"cdna_start": 1113,
"cds_end": null,
"cds_length": 1317,
"cds_start": 429,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047417682.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.429delG",
"hgvs_p": "p.Ile144fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047273638.1",
"strand": true,
"transcript": "XM_047417682.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 435,
"aa_ref": "G",
"aa_start": 140,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1612,
"cdna_start": 549,
"cds_end": null,
"cds_length": 1308,
"cds_start": 420,
"consequences": [
"frameshift_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047417683.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.420delG",
"hgvs_p": "p.Ile141fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047273639.1",
"strand": true,
"transcript": "XM_047417683.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 176,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 814,
"cdna_start": null,
"cds_end": null,
"cds_length": 531,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000936416.1",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "c.139-7442delG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606475.1",
"strand": true,
"transcript": "ENST00000936416.1",
"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": 3180,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000369407.3",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "n.2119delG",
"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": "ENST00000369407.3",
"transcript_support_level": 2
},
{
"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": 653,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000469443.2",
"gene_hgnc_id": 8923,
"gene_symbol": "PHGDH",
"hgvs_c": "n.534delG",
"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": "ENST00000469443.2",
"transcript_support_level": 2
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