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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: 11-34978135-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=34978135&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 34978135,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003477.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.976G>C",
"hgvs_p": "p.Val326Leu",
"transcript": "NM_003477.3",
"protein_id": "NP_003468.2",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 501,
"cds_start": 976,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000227868.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003477.3"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.976G>C",
"hgvs_p": "p.Val326Leu",
"transcript": "ENST00000227868.9",
"protein_id": "ENSP00000227868.4",
"transcript_support_level": 1,
"aa_start": 326,
"aa_end": null,
"aa_length": 501,
"cds_start": 976,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003477.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000227868.9"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.976G>C",
"hgvs_p": "p.Val326Leu",
"transcript": "ENST00000885501.1",
"protein_id": "ENSP00000555560.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 548,
"cds_start": 976,
"cds_end": null,
"cds_length": 1647,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885501.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.976G>C",
"hgvs_p": "p.Val326Leu",
"transcript": "ENST00000952507.1",
"protein_id": "ENSP00000622566.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 508,
"cds_start": 976,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952507.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.994G>C",
"hgvs_p": "p.Val332Leu",
"transcript": "ENST00000952504.1",
"protein_id": "ENSP00000622563.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 507,
"cds_start": 994,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952504.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.979G>C",
"hgvs_p": "p.Val327Leu",
"transcript": "ENST00000885499.1",
"protein_id": "ENSP00000555558.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 502,
"cds_start": 979,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885499.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.973G>C",
"hgvs_p": "p.Val325Leu",
"transcript": "ENST00000885497.1",
"protein_id": "ENSP00000555556.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 500,
"cds_start": 973,
"cds_end": null,
"cds_length": 1503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885497.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.973G>C",
"hgvs_p": "p.Val325Leu",
"transcript": "ENST00000885498.1",
"protein_id": "ENSP00000555557.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 500,
"cds_start": 973,
"cds_end": null,
"cds_length": 1503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885498.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.970G>C",
"hgvs_p": "p.Val324Leu",
"transcript": "ENST00000952503.1",
"protein_id": "ENSP00000622562.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 499,
"cds_start": 970,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952503.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.877G>C",
"hgvs_p": "p.Val293Leu",
"transcript": "ENST00000952501.1",
"protein_id": "ENSP00000622560.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 468,
"cds_start": 877,
"cds_end": null,
"cds_length": 1407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952501.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.976G>C",
"hgvs_p": "p.Val326Leu",
"transcript": "ENST00000952506.1",
"protein_id": "ENSP00000622565.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 448,
"cds_start": 976,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952506.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.796G>C",
"hgvs_p": "p.Val266Leu",
"transcript": "NM_001135024.2",
"protein_id": "NP_001128496.2",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 441,
"cds_start": 796,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001135024.2"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.796G>C",
"hgvs_p": "p.Val266Leu",
"transcript": "ENST00000448838.8",
"protein_id": "ENSP00000389404.3",
"transcript_support_level": 5,
"aa_start": 266,
"aa_end": null,
"aa_length": 441,
"cds_start": 796,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000448838.8"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.502G>C",
"hgvs_p": "p.Val168Leu",
"transcript": "ENST00000885500.1",
"protein_id": "ENSP00000555559.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 343,
"cds_start": 502,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885500.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.253G>C",
"hgvs_p": "p.Val85Leu",
"transcript": "ENST00000885503.1",
"protein_id": "ENSP00000555562.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 260,
"cds_start": 253,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885503.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.37G>C",
"hgvs_p": "p.Val13Leu",
"transcript": "ENST00000526309.1",
"protein_id": "ENSP00000433204.1",
"transcript_support_level": 3,
"aa_start": 13,
"aa_end": null,
"aa_length": 188,
"cds_start": 37,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000526309.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.796G>C",
"hgvs_p": "p.Val266Leu",
"transcript": "XM_011520390.2",
"protein_id": "XP_011518692.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 441,
"cds_start": 796,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011520390.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.965-6505G>C",
"hgvs_p": null,
"transcript": "ENST00000952505.1",
"protein_id": "ENSP00000622564.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 458,
"cds_start": null,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952505.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.343-6435G>C",
"hgvs_p": null,
"transcript": "NM_001166158.2",
"protein_id": "NP_001159630.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 274,
"cds_start": null,
"cds_end": null,
"cds_length": 825,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166158.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.343-6435G>C",
"hgvs_p": null,
"transcript": "ENST00000430469.6",
"protein_id": "ENSP00000415695.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 274,
"cds_start": null,
"cds_end": null,
"cds_length": 825,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000430469.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.337-6435G>C",
"hgvs_p": null,
"transcript": "ENST00000952502.1",
"protein_id": "ENSP00000622561.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 272,
"cds_start": null,
"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": "ENST00000952502.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "c.343-14180G>C",
"hgvs_p": null,
"transcript": "ENST00000885502.1",
"protein_id": "ENSP00000555561.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 221,
"cds_start": null,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885502.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"hgvs_c": "n.201G>C",
"hgvs_p": null,
"transcript": "ENST00000532159.1",
"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": "ENST00000532159.1"
}
],
"gene_symbol": "PDHX",
"gene_hgnc_id": 21350,
"dbsnp": "rs35560997",
"frequency_reference_population": 0.0068872957,
"hom_count_reference_population": 46,
"allele_count_reference_population": 10684,
"gnomad_exomes_af": 0.0070119,
"gnomad_genomes_af": 0.00574199,
"gnomad_exomes_ac": 9810,
"gnomad_genomes_ac": 874,
"gnomad_exomes_homalt": 42,
"gnomad_genomes_homalt": 4,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.014632463455200195,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.336,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3465,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.161,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_003477.3",
"gene_symbol": "PDHX",
"hgnc_id": 21350,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.976G>C",
"hgvs_p": "p.Val326Leu"
}
],
"clinvar_disease": "PDHX-related disorder,Pyruvate dehydrogenase E1-alpha deficiency,Pyruvate dehydrogenase E3-binding protein deficiency,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:5",
"phenotype_combined": "not specified|not provided|Pyruvate dehydrogenase E3-binding protein deficiency|Pyruvate dehydrogenase E1-alpha deficiency|PDHX-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}