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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: 14-50924018-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=50924018&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 50924018,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_002863.5",
"consequences": [
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "NM_002863.5",
"protein_id": "NP_002854.3",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 847,
"cds_start": 611,
"cds_end": null,
"cds_length": 2544,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000216392.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002863.5"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000216392.8",
"protein_id": "ENSP00000216392.7",
"transcript_support_level": 1,
"aa_start": 204,
"aa_end": null,
"aa_length": 847,
"cds_start": 611,
"cds_end": null,
"cds_length": 2544,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002863.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000216392.8"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000532462.5",
"protein_id": "ENSP00000431657.1",
"transcript_support_level": 1,
"aa_start": 204,
"aa_end": null,
"aa_length": 819,
"cds_start": 611,
"cds_end": null,
"cds_length": 2460,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000532462.5"
},
{
"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": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "n.678A>G",
"hgvs_p": null,
"transcript": "ENST00000530336.2",
"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": "ENST00000530336.2"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000874287.1",
"protein_id": "ENSP00000544346.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 852,
"cds_start": 611,
"cds_end": null,
"cds_length": 2559,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874287.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000874291.1",
"protein_id": "ENSP00000544350.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 850,
"cds_start": 611,
"cds_end": null,
"cds_length": 2553,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874291.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000941158.1",
"protein_id": "ENSP00000611217.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 846,
"cds_start": 611,
"cds_end": null,
"cds_length": 2541,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941158.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000874289.1",
"protein_id": "ENSP00000544348.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 844,
"cds_start": 611,
"cds_end": null,
"cds_length": 2535,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874289.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000941160.1",
"protein_id": "ENSP00000611219.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 844,
"cds_start": 611,
"cds_end": null,
"cds_length": 2535,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941160.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000941162.1",
"protein_id": "ENSP00000611221.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 839,
"cds_start": 611,
"cds_end": null,
"cds_length": 2520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941162.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000874290.1",
"protein_id": "ENSP00000544349.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 833,
"cds_start": 611,
"cds_end": null,
"cds_length": 2502,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874290.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000924121.1",
"protein_id": "ENSP00000594180.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 830,
"cds_start": 611,
"cds_end": null,
"cds_length": 2493,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924121.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000924124.1",
"protein_id": "ENSP00000594183.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 820,
"cds_start": 611,
"cds_end": null,
"cds_length": 2463,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924124.1"
},
{
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.509A>G",
"hgvs_p": "p.Tyr170Cys",
"transcript": "ENST00000941159.1",
"protein_id": "ENSP00000611218.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 818,
"cds_start": 509,
"cds_end": null,
"cds_length": 2457,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941159.1"
},
{
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.509A>G",
"hgvs_p": "p.Tyr170Cys",
"transcript": "NM_001163940.2",
"protein_id": "NP_001157412.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 813,
"cds_start": 509,
"cds_end": null,
"cds_length": 2442,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001163940.2"
},
{
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.509A>G",
"hgvs_p": "p.Tyr170Cys",
"transcript": "ENST00000544180.6",
"protein_id": "ENSP00000443787.1",
"transcript_support_level": 2,
"aa_start": 170,
"aa_end": null,
"aa_length": 813,
"cds_start": 509,
"cds_end": null,
"cds_length": 2442,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544180.6"
},
{
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000874286.1",
"protein_id": "ENSP00000544345.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 813,
"cds_start": 611,
"cds_end": null,
"cds_length": 2442,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874286.1"
},
{
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.509A>G",
"hgvs_p": "p.Tyr170Cys",
"transcript": "ENST00000924122.1",
"protein_id": "ENSP00000594181.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 810,
"cds_start": 509,
"cds_end": null,
"cds_length": 2433,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924122.1"
},
{
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys",
"transcript": "ENST00000924123.1",
"protein_id": "ENSP00000594182.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 782,
"cds_start": 611,
"cds_end": null,
"cds_length": 2349,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924123.1"
},
{
"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": 19,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.529-2951A>G",
"hgvs_p": null,
"transcript": "ENST00000924125.1",
"protein_id": "ENSP00000594184.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 803,
"cds_start": null,
"cds_end": null,
"cds_length": 2412,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924125.1"
},
{
"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": 18,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.427-2951A>G",
"hgvs_p": null,
"transcript": "ENST00000874288.1",
"protein_id": "ENSP00000544347.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 769,
"cds_start": null,
"cds_end": null,
"cds_length": 2310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874288.1"
},
{
"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": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"hgvs_c": "c.244-2951A>G",
"hgvs_p": null,
"transcript": "ENST00000941161.1",
"protein_id": "ENSP00000611220.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 708,
"cds_start": null,
"cds_end": null,
"cds_length": 2127,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941161.1"
}
],
"gene_symbol": "PYGL",
"gene_hgnc_id": 9725,
"dbsnp": "rs34096980",
"frequency_reference_population": 0.0029889771,
"hom_count_reference_population": 16,
"allele_count_reference_population": 4824,
"gnomad_exomes_af": 0.00305214,
"gnomad_genomes_af": 0.00238292,
"gnomad_exomes_ac": 4461,
"gnomad_genomes_ac": 363,
"gnomad_exomes_homalt": 13,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.059922605752944946,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.794,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2437,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.277,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": "Benign",
"acmg_criteria": "PP3,BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 9,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002863.5",
"gene_symbol": "PYGL",
"hgnc_id": 9725,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Tyr204Cys"
}
],
"clinvar_disease": " type VI,Glycogen storage disease,PYGL-related disorder,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:6",
"phenotype_combined": "Glycogen storage disease, type VI|not specified|not provided|PYGL-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}