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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
{
"variants": [
{
"chr": "X",
"pos": 19359612,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000422285.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1132C>T",
"hgvs_p": "p.Arg378Cys",
"transcript": "NM_000284.4",
"protein_id": "NP_000275.1",
"transcript_support_level": null,
"aa_start": 378,
"aa_end": null,
"aa_length": 390,
"cds_start": 1132,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 1243,
"cdna_end": null,
"cdna_length": 3349,
"mane_select": "ENST00000422285.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1132C>T",
"hgvs_p": "p.Arg378Cys",
"transcript": "ENST00000422285.7",
"protein_id": "ENSP00000394382.2",
"transcript_support_level": 1,
"aa_start": 378,
"aa_end": null,
"aa_length": 390,
"cds_start": 1132,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 1243,
"cdna_end": null,
"cdna_length": 3349,
"mane_select": "NM_000284.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1246C>T",
"hgvs_p": "p.Arg416Cys",
"transcript": "NM_001173454.2",
"protein_id": "NP_001166925.1",
"transcript_support_level": null,
"aa_start": 416,
"aa_end": null,
"aa_length": 428,
"cds_start": 1246,
"cds_end": null,
"cds_length": 1287,
"cdna_start": 1357,
"cdna_end": null,
"cdna_length": 3430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1246C>T",
"hgvs_p": "p.Arg416Cys",
"transcript": "ENST00000423505.6",
"protein_id": "ENSP00000406473.2",
"transcript_support_level": 2,
"aa_start": 416,
"aa_end": null,
"aa_length": 428,
"cds_start": 1246,
"cds_end": null,
"cds_length": 1287,
"cdna_start": 1357,
"cdna_end": null,
"cdna_length": 3463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1216C>T",
"hgvs_p": "p.Arg406Cys",
"transcript": "ENST00000417819.6",
"protein_id": "ENSP00000404616.2",
"transcript_support_level": 3,
"aa_start": 406,
"aa_end": null,
"aa_length": 418,
"cds_start": 1216,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 1291,
"cdna_end": null,
"cdna_length": 1518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1153C>T",
"hgvs_p": "p.Arg385Cys",
"transcript": "NM_001173455.2",
"protein_id": "NP_001166926.1",
"transcript_support_level": null,
"aa_start": 385,
"aa_end": null,
"aa_length": 397,
"cds_start": 1153,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 3337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1153C>T",
"hgvs_p": "p.Arg385Cys",
"transcript": "ENST00000355808.10",
"protein_id": "ENSP00000348062.6",
"transcript_support_level": 3,
"aa_start": 385,
"aa_end": null,
"aa_length": 397,
"cds_start": 1153,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 3330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347Cys",
"transcript": "NM_001173456.2",
"protein_id": "NP_001166927.1",
"transcript_support_level": null,
"aa_start": 347,
"aa_end": null,
"aa_length": 359,
"cds_start": 1039,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1150,
"cdna_end": null,
"cdna_length": 3223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347Cys",
"transcript": "ENST00000540249.5",
"protein_id": "ENSP00000440761.1",
"transcript_support_level": 2,
"aa_start": 347,
"aa_end": null,
"aa_length": 359,
"cds_start": 1039,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 3277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "c.1153C>T",
"hgvs_p": "p.Arg385Cys",
"transcript": "XM_017029574.3",
"protein_id": "XP_016885063.1",
"transcript_support_level": null,
"aa_start": 385,
"aa_end": null,
"aa_length": 397,
"cds_start": 1153,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 3370,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "n.477C>T",
"hgvs_p": null,
"transcript": "ENST00000379804.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 709,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "n.*824C>T",
"hgvs_p": null,
"transcript": "ENST00000379805.4",
"protein_id": "ENSP00000369133.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "n.571C>T",
"hgvs_p": null,
"transcript": "ENST00000478795.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "n.927C>T",
"hgvs_p": null,
"transcript": "ENST00000481733.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "n.*464C>T",
"hgvs_p": null,
"transcript": "ENST00000696704.1",
"protein_id": "ENSP00000512823.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "n.*587C>T",
"hgvs_p": null,
"transcript": "ENST00000696705.1",
"protein_id": "ENSP00000512824.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3257,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "n.*824C>T",
"hgvs_p": null,
"transcript": "ENST00000379805.4",
"protein_id": "ENSP00000369133.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "n.*464C>T",
"hgvs_p": null,
"transcript": "ENST00000696704.1",
"protein_id": "ENSP00000512823.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"hgvs_c": "n.*587C>T",
"hgvs_p": null,
"transcript": "ENST00000696705.1",
"protein_id": "ENSP00000512824.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3257,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDHA1",
"gene_hgnc_id": 8806,
"dbsnp": "rs863224147",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.972939133644104,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.907,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8691,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.48,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.695,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3,PP4,PM6_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PM5",
"PP3",
"PP4",
"PM6_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000422285.7",
"gene_symbol": "PDHA1",
"hgnc_id": 8806,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.1132C>T",
"hgvs_p": "p.Arg378Cys"
}
],
"clinvar_disease": "Pyruvate dehydrogenase E1-alpha deficiency,Pyruvate dehydrogenase complex deficiency,SUDDEN INFANT DEATH SYNDROME,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:8",
"phenotype_combined": "not provided|Pyruvate dehydrogenase E1-alpha deficiency|SUDDEN INFANT DEATH SYNDROME|Pyruvate dehydrogenase complex deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}