← Back to variant description
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: 3-58428064-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=58428064&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 58428064,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000925.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.1050A>G",
"hgvs_p": "p.Ile350Met",
"transcript": "NM_000925.4",
"protein_id": "NP_000916.2",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 359,
"cds_start": 1050,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1073,
"cdna_end": null,
"cdna_length": 1507,
"mane_select": "ENST00000302746.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000925.4"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.1050A>G",
"hgvs_p": "p.Ile350Met",
"transcript": "ENST00000302746.11",
"protein_id": "ENSP00000307241.6",
"transcript_support_level": 1,
"aa_start": 350,
"aa_end": null,
"aa_length": 359,
"cds_start": 1050,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1073,
"cdna_end": null,
"cdna_length": 1507,
"mane_select": "NM_000925.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000302746.11"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.996A>G",
"hgvs_p": "p.Ile332Met",
"transcript": "ENST00000383714.8",
"protein_id": "ENSP00000373220.4",
"transcript_support_level": 1,
"aa_start": 332,
"aa_end": null,
"aa_length": 341,
"cds_start": 996,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 1044,
"cdna_end": null,
"cdna_length": 1478,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.1163A>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": 1535,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000461692.5"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.1038A>G",
"hgvs_p": "p.Ile346Met",
"transcript": "ENST00000962538.1",
"protein_id": "ENSP00000632597.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 355,
"cds_start": 1038,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 1052,
"cdna_end": null,
"cdna_length": 1483,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962538.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.1029A>G",
"hgvs_p": "p.Ile343Met",
"transcript": "ENST00000909150.1",
"protein_id": "ENSP00000579209.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 352,
"cds_start": 1029,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 1232,
"cdna_end": null,
"cdna_length": 1665,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909150.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.1014A>G",
"hgvs_p": "p.Ile338Met",
"transcript": "ENST00000909156.1",
"protein_id": "ENSP00000579215.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 347,
"cds_start": 1014,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 1040,
"cdna_end": null,
"cdna_length": 1417,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909156.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.996A>G",
"hgvs_p": "p.Ile332Met",
"transcript": "NM_001173468.2",
"protein_id": "NP_001166939.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 341,
"cds_start": 996,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 1453,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001173468.2"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.996A>G",
"hgvs_p": "p.Ile332Met",
"transcript": "NM_001315536.2",
"protein_id": "NP_001302465.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 341,
"cds_start": 996,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 1453,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001315536.2"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.996A>G",
"hgvs_p": "p.Ile332Met",
"transcript": "ENST00000485460.5",
"protein_id": "ENSP00000417267.1",
"transcript_support_level": 2,
"aa_start": 332,
"aa_end": null,
"aa_length": 341,
"cds_start": 996,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 1005,
"cdna_end": null,
"cdna_length": 1397,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000485460.5"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.987A>G",
"hgvs_p": "p.Ile329Met",
"transcript": "ENST00000909153.1",
"protein_id": "ENSP00000579211.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 338,
"cds_start": 987,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 1017,
"cdna_end": null,
"cdna_length": 1448,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909153.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.951A>G",
"hgvs_p": "p.Ile317Met",
"transcript": "ENST00000909152.1",
"protein_id": "ENSP00000579210.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 326,
"cds_start": 951,
"cds_end": null,
"cds_length": 981,
"cdna_start": 992,
"cdna_end": null,
"cdna_length": 1425,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909152.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Ile299Met",
"transcript": "ENST00000909157.1",
"protein_id": "ENSP00000579216.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 308,
"cds_start": 897,
"cds_end": null,
"cds_length": 927,
"cdna_start": 910,
"cdna_end": null,
"cdna_length": 1293,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909157.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.843A>G",
"hgvs_p": "p.Ile281Met",
"transcript": "ENST00000909154.1",
"protein_id": "ENSP00000579213.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 290,
"cds_start": 843,
"cds_end": null,
"cds_length": 873,
"cdna_start": 866,
"cdna_end": null,
"cdna_length": 1299,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909154.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.789A>G",
"hgvs_p": "p.Ile263Met",
"transcript": "ENST00000962539.1",
"protein_id": "ENSP00000632598.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 272,
"cds_start": 789,
"cds_end": null,
"cds_length": 819,
"cdna_start": 798,
"cdna_end": null,
"cdna_length": 1231,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962539.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.561A>G",
"hgvs_p": "p.Ile187Met",
"transcript": "ENST00000909155.1",
"protein_id": "ENSP00000579214.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 196,
"cds_start": 561,
"cds_end": null,
"cds_length": 591,
"cdna_start": 576,
"cdna_end": null,
"cdna_length": 1008,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909155.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "c.*64A>G",
"hgvs_p": null,
"transcript": "ENST00000474765.1",
"protein_id": "ENSP00000418448.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 350,
"cds_start": null,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1503,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000474765.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.*436A>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": 1616,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.4076A>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": 4459,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.1156A>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": 1590,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033384.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"hgvs_c": "n.*436A>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": 1616,
"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": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272182",
"gene_hgnc_id": null,
"hgvs_c": "n.-191T>C",
"hgvs_p": null,
"transcript": "ENST00000607214.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 561,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000607214.1"
}
],
"gene_symbol": "PDHB",
"gene_hgnc_id": 8808,
"dbsnp": "rs1641509410",
"frequency_reference_population": 6.864671e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.86467e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.397907555103302,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.458,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2138,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.158,
"phylop100way_prediction": "Benign",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000925.4",
"gene_symbol": "PDHB",
"hgnc_id": 8808,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1050A>G",
"hgvs_p": "p.Ile350Met"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000607214.1",
"gene_symbol": "ENSG00000272182",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-191T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Pyruvate dehydrogenase E1-beta deficiency,Pyruvate dehydrogenase phosphatase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Pyruvate dehydrogenase E1-beta deficiency|Pyruvate dehydrogenase phosphatase deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}