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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: 11-799453-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=799453&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 799453,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_145886.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2587C>T",
"hgvs_p": "p.Gln863*",
"transcript": "NM_145886.4",
"protein_id": "NP_665893.2",
"transcript_support_level": null,
"aa_start": 863,
"aa_end": null,
"aa_length": 910,
"cds_start": 2587,
"cds_end": null,
"cds_length": 2733,
"cdna_start": 2715,
"cdna_end": null,
"cdna_length": 2984,
"mane_select": "ENST00000347755.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_145886.4"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2587C>T",
"hgvs_p": "p.Gln863*",
"transcript": "ENST00000347755.10",
"protein_id": "ENSP00000337797.5",
"transcript_support_level": 1,
"aa_start": 863,
"aa_end": null,
"aa_length": 910,
"cds_start": 2587,
"cds_end": null,
"cds_length": 2733,
"cdna_start": 2715,
"cdna_end": null,
"cdna_length": 2984,
"mane_select": "NM_145886.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000347755.10"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2536C>T",
"hgvs_p": "p.Gln846*",
"transcript": "ENST00000411829.6",
"protein_id": "ENSP00000416801.2",
"transcript_support_level": 1,
"aa_start": 846,
"aa_end": null,
"aa_length": 893,
"cds_start": 2536,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 2617,
"cdna_end": null,
"cdna_length": 2886,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000411829.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "n.*2287C>T",
"hgvs_p": null,
"transcript": "ENST00000525028.6",
"protein_id": "ENSP00000436342.1",
"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": 3175,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000525028.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "n.*2287C>T",
"hgvs_p": null,
"transcript": "ENST00000525028.6",
"protein_id": "ENSP00000436342.1",
"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": 3175,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000525028.6"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2536C>T",
"hgvs_p": "p.Gln846*",
"transcript": "NM_145887.4",
"protein_id": "NP_665894.2",
"transcript_support_level": null,
"aa_start": 846,
"aa_end": null,
"aa_length": 893,
"cds_start": 2536,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 2664,
"cdna_end": null,
"cdna_length": 2933,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_145887.4"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2740C>T",
"hgvs_p": "p.Gln914*",
"transcript": "XM_047427238.1",
"protein_id": "XP_047283194.1",
"transcript_support_level": null,
"aa_start": 914,
"aa_end": null,
"aa_length": 961,
"cds_start": 2740,
"cds_end": null,
"cds_length": 2886,
"cdna_start": 3289,
"cdna_end": null,
"cdna_length": 3558,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047427238.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2689C>T",
"hgvs_p": "p.Gln897*",
"transcript": "XM_047427239.1",
"protein_id": "XP_047283195.1",
"transcript_support_level": null,
"aa_start": 897,
"aa_end": null,
"aa_length": 944,
"cds_start": 2689,
"cds_end": null,
"cds_length": 2835,
"cdna_start": 3238,
"cdna_end": null,
"cdna_length": 3507,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047427239.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2668C>T",
"hgvs_p": "p.Gln890*",
"transcript": "XM_047427240.1",
"protein_id": "XP_047283196.1",
"transcript_support_level": null,
"aa_start": 890,
"aa_end": null,
"aa_length": 937,
"cds_start": 2668,
"cds_end": null,
"cds_length": 2814,
"cdna_start": 3217,
"cdna_end": null,
"cdna_length": 3486,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047427240.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2659C>T",
"hgvs_p": "p.Gln887*",
"transcript": "XM_005253005.6",
"protein_id": "XP_005253062.1",
"transcript_support_level": null,
"aa_start": 887,
"aa_end": null,
"aa_length": 934,
"cds_start": 2659,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 3741,
"cdna_end": null,
"cdna_length": 4010,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005253005.6"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2659C>T",
"hgvs_p": "p.Gln887*",
"transcript": "XM_005253006.6",
"protein_id": "XP_005253063.1",
"transcript_support_level": null,
"aa_start": 887,
"aa_end": null,
"aa_length": 934,
"cds_start": 2659,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 2850,
"cdna_end": null,
"cdna_length": 3119,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005253006.6"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2617C>T",
"hgvs_p": "p.Gln873*",
"transcript": "XM_011520209.4",
"protein_id": "XP_011518511.1",
"transcript_support_level": null,
"aa_start": 873,
"aa_end": null,
"aa_length": 920,
"cds_start": 2617,
"cds_end": null,
"cds_length": 2763,
"cdna_start": 3166,
"cdna_end": null,
"cdna_length": 3435,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011520209.4"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2587C>T",
"hgvs_p": "p.Gln863*",
"transcript": "XM_011520210.4",
"protein_id": "XP_011518512.1",
"transcript_support_level": null,
"aa_start": 863,
"aa_end": null,
"aa_length": 910,
"cds_start": 2587,
"cds_end": null,
"cds_length": 2733,
"cdna_start": 3669,
"cdna_end": null,
"cdna_length": 3938,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011520210.4"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2221C>T",
"hgvs_p": "p.Gln741*",
"transcript": "XM_011520212.3",
"protein_id": "XP_011518514.1",
"transcript_support_level": null,
"aa_start": 741,
"aa_end": null,
"aa_length": 788,
"cds_start": 2221,
"cds_end": null,
"cds_length": 2367,
"cdna_start": 2513,
"cdna_end": null,
"cdna_length": 2782,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011520212.3"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2170C>T",
"hgvs_p": "p.Gln724*",
"transcript": "XM_047427241.1",
"protein_id": "XP_047283197.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 771,
"cds_start": 2170,
"cds_end": null,
"cds_length": 2316,
"cdna_start": 2462,
"cdna_end": null,
"cdna_length": 2731,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047427241.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2149C>T",
"hgvs_p": "p.Gln717*",
"transcript": "XM_047427242.1",
"protein_id": "XP_047283198.1",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 764,
"cds_start": 2149,
"cds_end": null,
"cds_length": 2295,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 2710,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047427242.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.2098C>T",
"hgvs_p": "p.Gln700*",
"transcript": "XM_047427243.1",
"protein_id": "XP_047283199.1",
"transcript_support_level": null,
"aa_start": 700,
"aa_end": null,
"aa_length": 747,
"cds_start": 2098,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 2390,
"cdna_end": null,
"cdna_length": 2659,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047427243.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.1720C>T",
"hgvs_p": "p.Gln574*",
"transcript": "XM_011520213.3",
"protein_id": "XP_011518515.1",
"transcript_support_level": null,
"aa_start": 574,
"aa_end": null,
"aa_length": 621,
"cds_start": 1720,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 2026,
"cdna_end": null,
"cdna_length": 2295,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011520213.3"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.1720C>T",
"hgvs_p": "p.Gln574*",
"transcript": "XM_047427245.1",
"protein_id": "XP_047283201.1",
"transcript_support_level": null,
"aa_start": 574,
"aa_end": null,
"aa_length": 621,
"cds_start": 1720,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 2237,
"cdna_end": null,
"cdna_length": 2506,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047427245.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "c.1648C>T",
"hgvs_p": "p.Gln550*",
"transcript": "XM_047427246.1",
"protein_id": "XP_047283202.1",
"transcript_support_level": null,
"aa_start": 550,
"aa_end": null,
"aa_length": 597,
"cds_start": 1648,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1954,
"cdna_end": null,
"cdna_length": 2223,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047427246.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPLP2",
"gene_hgnc_id": 10377,
"hgvs_c": "c.-1476G>A",
"hgvs_p": null,
"transcript": "ENST00000960563.1",
"protein_id": "ENSP00000630622.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 115,
"cds_start": null,
"cds_end": null,
"cds_length": 348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1899,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960563.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIDD1",
"gene_hgnc_id": 16491,
"hgvs_c": "n.*2602C>T",
"hgvs_p": null,
"transcript": "ENST00000524486.5",
"protein_id": "ENSP00000436146.1",
"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,
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],
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"gnomad_exomes_homalt": 0,
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"computational_score_selected": 0.5099999904632568,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"alphamissense_score": null,
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"bayesdelnoaf_score": 0.51,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.745,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
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"acmg_by_gene": [
{
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"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_145886.4",
"gene_symbol": "PIDD1",
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"effects": [
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"inheritance_mode": "AR",
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"hgvs_p": "p.Gln863*"
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{
"score": 7,
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"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000960563.1",
"gene_symbol": "RPLP2",
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"inheritance_mode": "AD",
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}
],
"clinvar_disease": " autosomal recessive 75, with neuropsychiatric features and variant lissencephaly,Intellectual developmental disorder,Intellectual disability",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Intellectual disability|Intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}