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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: X-19359612-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=19359612&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3",
"PP4",
"PM6_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PDHA1",
"hgnc_id": 8806,
"hgvs_c": "c.1246C>T",
"hgvs_p": "p.Arg416Cys",
"inheritance_mode": "AR,XL",
"pathogenic_score": 10,
"score": 10,
"transcript": "NM_001173454.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3,PP4,PM6_Strong",
"acmg_score": 10,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.8691,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.48,
"chr": "X",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Pyruvate dehydrogenase E1-alpha deficiency,Pyruvate dehydrogenase complex deficiency,SUDDEN INFANT DEATH SYNDROME,not provided",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:8",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.972939133644104,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 390,
"aa_ref": "R",
"aa_start": 378,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3349,
"cdna_start": 1243,
"cds_end": null,
"cds_length": 1173,
"cds_start": 1132,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_000284.4",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1132C>T",
"hgvs_p": "p.Arg378Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000422285.7",
"protein_coding": true,
"protein_id": "NP_000275.1",
"strand": true,
"transcript": "NM_000284.4",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 390,
"aa_ref": "R",
"aa_start": 378,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3349,
"cdna_start": 1243,
"cds_end": null,
"cds_length": 1173,
"cds_start": 1132,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000422285.7",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1132C>T",
"hgvs_p": "p.Arg378Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000284.4",
"protein_coding": true,
"protein_id": "ENSP00000394382.2",
"strand": true,
"transcript": "ENST00000422285.7",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 456,
"aa_ref": "R",
"aa_start": 444,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3545,
"cdna_start": 1474,
"cds_end": null,
"cds_length": 1371,
"cds_start": 1330,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000947567.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1330C>T",
"hgvs_p": "p.Arg444Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617626.1",
"strand": true,
"transcript": "ENST00000947567.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 443,
"aa_ref": "R",
"aa_start": 431,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1586,
"cdna_start": 1353,
"cds_end": null,
"cds_length": 1332,
"cds_start": 1291,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000947577.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1291C>T",
"hgvs_p": "p.Arg431Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617636.1",
"strand": true,
"transcript": "ENST00000947577.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 424,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3445,
"cdna_start": 1378,
"cds_end": null,
"cds_length": 1311,
"cds_start": 1270,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000881112.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1270C>T",
"hgvs_p": "p.Arg424Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551171.1",
"strand": true,
"transcript": "ENST00000881112.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 435,
"aa_ref": "R",
"aa_start": 423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1610,
"cdna_start": 1369,
"cds_end": null,
"cds_length": 1308,
"cds_start": 1267,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000881116.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1267C>T",
"hgvs_p": "p.Arg423Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551175.1",
"strand": true,
"transcript": "ENST00000881116.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 428,
"aa_ref": "R",
"aa_start": 416,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3430,
"cdna_start": 1357,
"cds_end": null,
"cds_length": 1287,
"cds_start": 1246,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001173454.2",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1246C>T",
"hgvs_p": "p.Arg416Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001166925.1",
"strand": true,
"transcript": "NM_001173454.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 428,
"aa_ref": "R",
"aa_start": 416,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3463,
"cdna_start": 1357,
"cds_end": null,
"cds_length": 1287,
"cds_start": 1246,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000423505.6",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1246C>T",
"hgvs_p": "p.Arg416Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000406473.2",
"strand": true,
"transcript": "ENST00000423505.6",
"transcript_support_level": 2
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 418,
"aa_ref": "R",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1518,
"cdna_start": 1291,
"cds_end": null,
"cds_length": 1257,
"cds_start": 1216,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000417819.6",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1216C>T",
"hgvs_p": "p.Arg406Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000404616.2",
"strand": true,
"transcript": "ENST00000417819.6",
"transcript_support_level": 3
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 412,
"aa_ref": "R",
"aa_start": 400,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1546,
"cdna_start": 1304,
"cds_end": null,
"cds_length": 1239,
"cds_start": 1198,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000947571.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1198C>T",
"hgvs_p": "p.Arg400Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617630.1",
"strand": true,
"transcript": "ENST00000947571.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 405,
"aa_ref": "R",
"aa_start": 393,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1536,
"cdna_start": 1304,
"cds_end": null,
"cds_length": 1218,
"cds_start": 1177,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000881114.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1177C>T",
"hgvs_p": "p.Arg393Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551173.1",
"strand": true,
"transcript": "ENST00000881114.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 404,
"aa_ref": "R",
"aa_start": 392,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3337,
"cdna_start": 1264,
"cds_end": null,
"cds_length": 1215,
"cds_start": 1174,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000927451.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1174C>T",
"hgvs_p": "p.Arg392Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000597510.1",
"strand": true,
"transcript": "ENST00000927451.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 400,
"aa_ref": "R",
"aa_start": 388,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1466,
"cdna_start": 1238,
"cds_end": null,
"cds_length": 1203,
"cds_start": 1162,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000947576.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1162C>T",
"hgvs_p": "p.Arg388Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617635.1",
"strand": true,
"transcript": "ENST00000947576.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 397,
"aa_ref": "R",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3337,
"cdna_start": 1264,
"cds_end": null,
"cds_length": 1194,
"cds_start": 1153,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001173455.2",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1153C>T",
"hgvs_p": "p.Arg385Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001166926.1",
"strand": true,
"transcript": "NM_001173455.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 397,
"aa_ref": "R",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3330,
"cdna_start": 1264,
"cds_end": null,
"cds_length": 1194,
"cds_start": 1153,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000355808.10",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1153C>T",
"hgvs_p": "p.Arg385Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000348062.6",
"strand": true,
"transcript": "ENST00000355808.10",
"transcript_support_level": 3
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 397,
"aa_ref": "R",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1485,
"cdna_start": 1259,
"cds_end": null,
"cds_length": 1194,
"cds_start": 1153,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000881118.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1153C>T",
"hgvs_p": "p.Arg385Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551177.1",
"strand": true,
"transcript": "ENST00000881118.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 391,
"aa_ref": "R",
"aa_start": 379,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1484,
"cdna_start": 1246,
"cds_end": null,
"cds_length": 1176,
"cds_start": 1135,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000881115.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1135C>T",
"hgvs_p": "p.Arg379Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551174.1",
"strand": true,
"transcript": "ENST00000881115.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 388,
"aa_ref": "R",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3306,
"cdna_start": 1236,
"cds_end": null,
"cds_length": 1167,
"cds_start": 1126,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000947570.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1126C>T",
"hgvs_p": "p.Arg376Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617629.1",
"strand": true,
"transcript": "ENST00000947570.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 387,
"aa_ref": "R",
"aa_start": 375,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3317,
"cdna_start": 1234,
"cds_end": null,
"cds_length": 1164,
"cds_start": 1123,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000947568.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1123C>T",
"hgvs_p": "p.Arg375Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617627.1",
"strand": true,
"transcript": "ENST00000947568.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 381,
"aa_ref": "R",
"aa_start": 369,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1439,
"cdna_start": 1197,
"cds_end": null,
"cds_length": 1146,
"cds_start": 1105,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000947573.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "c.1105C>T",
"hgvs_p": "p.Arg369Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617632.1",
"strand": true,
"transcript": "ENST00000947573.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 370,
"aa_ref": "R",
"aa_start": 358,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1426,
"cdna_start": 1183,
"cds_end": null,
"cds_length": 1113,
"cds_start": 1072,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
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"feature": "ENST00000696705.1",
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"hgvs_c": "n.*587C>T",
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"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000512824.1",
"strand": true,
"transcript": "ENST00000696705.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs863224147",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 8806,
"gene_symbol": "PDHA1",
"gnomad_exomes_ac": null,
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"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "not provided|Pyruvate dehydrogenase E1-alpha deficiency|SUDDEN INFANT DEATH SYNDROME|Pyruvate dehydrogenase complex deficiency",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.695,
"pos": 19359612,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.907,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001173454.2"
}
]
}