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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: 14-50915465-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=50915465&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PYGL",
"hgnc_id": 9725,
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"inheritance_mode": "AR",
"pathogenic_score": 1,
"score": 1,
"transcript": "NM_002863.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3",
"acmg_score": 1,
"allele_count_reference_population": 374,
"alphamissense_prediction": null,
"alphamissense_score": 0.22,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.06,
"chr": "14",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " type VI,Glycogen storage disease,Inborn genetic diseases,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.7516698837280273,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 847,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2799,
"cdna_start": 1354,
"cds_end": null,
"cds_length": 2544,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_002863.5",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000216392.8",
"protein_coding": true,
"protein_id": "NP_002854.3",
"strand": false,
"transcript": "NM_002863.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 847,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2799,
"cdna_start": 1354,
"cds_end": null,
"cds_length": 2544,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000216392.8",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002863.5",
"protein_coding": true,
"protein_id": "ENSP00000216392.7",
"strand": false,
"transcript": "ENST00000216392.8",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 819,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2711,
"cdna_start": 1327,
"cds_end": null,
"cds_length": 2460,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000532462.5",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000431657.1",
"strand": false,
"transcript": "ENST00000532462.5",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 852,
"aa_ref": "R",
"aa_start": 430,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2814,
"cdna_start": 1369,
"cds_end": null,
"cds_length": 2559,
"cds_start": 1289,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000874287.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1289G>A",
"hgvs_p": "p.Arg430His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544346.1",
"strand": false,
"transcript": "ENST00000874287.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 850,
"aa_ref": "R",
"aa_start": 428,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2806,
"cdna_start": 1363,
"cds_end": null,
"cds_length": 2553,
"cds_start": 1283,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000874291.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1283G>A",
"hgvs_p": "p.Arg428His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544350.1",
"strand": false,
"transcript": "ENST00000874291.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 846,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3046,
"cdna_start": 1605,
"cds_end": null,
"cds_length": 2541,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000941158.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611217.1",
"strand": false,
"transcript": "ENST00000941158.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 844,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2790,
"cdna_start": 1354,
"cds_end": null,
"cds_length": 2535,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000874289.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544348.1",
"strand": false,
"transcript": "ENST00000874289.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 844,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2770,
"cdna_start": 1335,
"cds_end": null,
"cds_length": 2535,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000941160.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611219.1",
"strand": false,
"transcript": "ENST00000941160.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 839,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2729,
"cdna_start": 1311,
"cds_end": null,
"cds_length": 2520,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000941162.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611221.1",
"strand": false,
"transcript": "ENST00000941162.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 833,
"aa_ref": "R",
"aa_start": 411,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2756,
"cdna_start": 1312,
"cds_end": null,
"cds_length": 2502,
"cds_start": 1232,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000874290.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1232G>A",
"hgvs_p": "p.Arg411His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544349.1",
"strand": false,
"transcript": "ENST00000874290.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 830,
"aa_ref": "R",
"aa_start": 411,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2841,
"cdna_start": 1409,
"cds_end": null,
"cds_length": 2493,
"cds_start": 1232,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000924121.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1232G>A",
"hgvs_p": "p.Arg411His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594180.1",
"strand": false,
"transcript": "ENST00000924121.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 820,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2716,
"cdna_start": 1354,
"cds_end": null,
"cds_length": 2463,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000924124.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594183.1",
"strand": false,
"transcript": "ENST00000924124.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 818,
"aa_ref": "R",
"aa_start": 396,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2708,
"cdna_start": 1267,
"cds_end": null,
"cds_length": 2457,
"cds_start": 1187,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000941159.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1187G>A",
"hgvs_p": "p.Arg396His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611218.1",
"strand": false,
"transcript": "ENST00000941159.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 813,
"aa_ref": "R",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2697,
"cdna_start": 1252,
"cds_end": null,
"cds_length": 2442,
"cds_start": 1172,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001163940.2",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1172G>A",
"hgvs_p": "p.Arg391His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001157412.1",
"strand": false,
"transcript": "NM_001163940.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 813,
"aa_ref": "R",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2696,
"cdna_start": 1252,
"cds_end": null,
"cds_length": 2442,
"cds_start": 1172,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000544180.6",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1172G>A",
"hgvs_p": "p.Arg391His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443787.1",
"strand": false,
"transcript": "ENST00000544180.6",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 813,
"aa_ref": "R",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2699,
"cdna_start": 1356,
"cds_end": null,
"cds_length": 2442,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000874286.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1274G>A",
"hgvs_p": "p.Arg425His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544345.1",
"strand": false,
"transcript": "ENST00000874286.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 810,
"aa_ref": "R",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2689,
"cdna_start": 1253,
"cds_end": null,
"cds_length": 2433,
"cds_start": 1172,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000924122.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1172G>A",
"hgvs_p": "p.Arg391His",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594181.1",
"strand": false,
"transcript": "ENST00000924122.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
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"aa_length": 803,
"aa_ref": "R",
"aa_start": 381,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2648,
"cdna_start": 1203,
"cds_end": null,
"cds_length": 2412,
"cds_start": 1142,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000924125.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1142G>A",
"hgvs_p": "p.Arg381His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594184.1",
"strand": false,
"transcript": "ENST00000924125.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
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"aa_length": 782,
"aa_ref": "R",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2602,
"cdna_start": 1159,
"cds_end": null,
"cds_length": 2349,
"cds_start": 1079,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000924123.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1079G>A",
"hgvs_p": "p.Arg360His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594182.1",
"strand": false,
"transcript": "ENST00000924123.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 769,
"aa_ref": "R",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2565,
"cdna_start": 1120,
"cds_end": null,
"cds_length": 2310,
"cds_start": 1040,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000874288.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.1040G>A",
"hgvs_p": "p.Arg347His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544347.1",
"strand": false,
"transcript": "ENST00000874288.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 708,
"aa_ref": "R",
"aa_start": 286,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2338,
"cdna_start": 899,
"cds_end": null,
"cds_length": 2127,
"cds_start": 857,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000941161.1",
"gene_hgnc_id": 9725,
"gene_symbol": "PYGL",
"hgvs_c": "c.857G>A",
"hgvs_p": "p.Arg286His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
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},
{
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],
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"feature": "ENST00000528757.2",
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}
],
"custom_annotations": null,
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"dbsnp": "rs2228499",
"effect": "missense_variant",
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"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Glycogen storage disease, type VI|not provided|Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
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"ref": "C",
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"splice_source_selected": "max_spliceai",
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}
]
}