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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: 3-58430851-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=58430851&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 58430851,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000925.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.395A>G",
"hgvs_p": "p.Tyr132Cys",
"transcript": "NM_000925.4",
"protein_id": "NP_000916.2",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 359,
"cds_start": 395,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000302746.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000925.4"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.395A>G",
"hgvs_p": "p.Tyr132Cys",
"transcript": "ENST00000302746.11",
"protein_id": "ENSP00000307241.6",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 359,
"cds_start": 395,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000925.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000302746.11"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.Tyr114Cys",
"transcript": "ENST00000383714.8",
"protein_id": "ENSP00000373220.4",
"transcript_support_level": 1,
"aa_start": 114,
"aa_end": null,
"aa_length": 341,
"cds_start": 341,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000383714.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.508A>G",
"hgvs_p": null,
"transcript": "ENST00000461692.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000461692.5"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.395A>G",
"hgvs_p": "p.Tyr132Cys",
"transcript": "ENST00000962538.1",
"protein_id": "ENSP00000632597.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 355,
"cds_start": 395,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962538.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.374A>G",
"hgvs_p": "p.Tyr125Cys",
"transcript": "ENST00000909150.1",
"protein_id": "ENSP00000579209.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 352,
"cds_start": 374,
"cds_end": null,
"cds_length": 1059,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909150.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.Tyr114Cys",
"transcript": "ENST00000474765.1",
"protein_id": "ENSP00000418448.1",
"transcript_support_level": 5,
"aa_start": 114,
"aa_end": null,
"aa_length": 350,
"cds_start": 341,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000474765.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.359A>G",
"hgvs_p": "p.Tyr120Cys",
"transcript": "ENST00000909156.1",
"protein_id": "ENSP00000579215.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 347,
"cds_start": 359,
"cds_end": null,
"cds_length": 1044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909156.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.395A>G",
"hgvs_p": "p.Tyr132Cys",
"transcript": "NM_001173468.2",
"protein_id": "NP_001166939.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 341,
"cds_start": 395,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001173468.2"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.Tyr114Cys",
"transcript": "NM_001315536.2",
"protein_id": "NP_001302465.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 341,
"cds_start": 341,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001315536.2"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.395A>G",
"hgvs_p": "p.Tyr132Cys",
"transcript": "ENST00000485460.5",
"protein_id": "ENSP00000417267.1",
"transcript_support_level": 2,
"aa_start": 132,
"aa_end": null,
"aa_length": 341,
"cds_start": 395,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000485460.5"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.332A>G",
"hgvs_p": "p.Tyr111Cys",
"transcript": "ENST00000909153.1",
"protein_id": "ENSP00000579211.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 338,
"cds_start": 332,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909153.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.296A>G",
"hgvs_p": "p.Tyr99Cys",
"transcript": "ENST00000909152.1",
"protein_id": "ENSP00000579210.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 326,
"cds_start": 296,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909152.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.242A>G",
"hgvs_p": "p.Tyr81Cys",
"transcript": "ENST00000909157.1",
"protein_id": "ENSP00000579216.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 308,
"cds_start": 242,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909157.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.188A>G",
"hgvs_p": "p.Tyr63Cys",
"transcript": "ENST00000909154.1",
"protein_id": "ENSP00000579213.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 290,
"cds_start": 188,
"cds_end": null,
"cds_length": 873,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909154.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.134A>G",
"hgvs_p": "p.Tyr45Cys",
"transcript": "ENST00000962539.1",
"protein_id": "ENSP00000632598.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 272,
"cds_start": 134,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962539.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.303+742A>G",
"hgvs_p": null,
"transcript": "ENST00000909155.1",
"protein_id": "ENSP00000579214.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 196,
"cds_start": null,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909155.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.395A>G",
"hgvs_p": null,
"transcript": "ENST00000469364.5",
"protein_id": "ENSP00000419580.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000469364.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.2800A>G",
"hgvs_p": null,
"transcript": "ENST00000479945.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000479945.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.487A>G",
"hgvs_p": null,
"transcript": "ENST00000480626.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000480626.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.501A>G",
"hgvs_p": null,
"transcript": "NR_033384.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033384.2"
}
],
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"dbsnp": "rs28935769",
"frequency_reference_population": 0.000001368298,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000013683,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9904555678367615,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.966,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7804,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.462,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.05,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000925.4",
"gene_symbol": "PDHB",
"hgnc_id": 8808,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.395A>G",
"hgvs_p": "p.Tyr132Cys"
}
],
"clinvar_disease": "Pyruvate dehydrogenase E1-beta deficiency",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Pyruvate dehydrogenase E1-beta deficiency",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}