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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: 3-136002194-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=136002194&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 14,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BA1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "PPP2R3A",
"hgnc_id": 9307,
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -14,
"transcript": "NM_002718.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BA1",
"acmg_score": -14,
"allele_count_reference_population": 119226,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.53,
"chr": "3",
"clinvar_classification": "Benign",
"clinvar_disease": "PPP2R3A-related disorder",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5299999713897705,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1150,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6743,
"cdna_start": 1258,
"cds_end": null,
"cds_length": 3453,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_002718.5",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264977.8",
"protein_coding": true,
"protein_id": "NP_002709.2",
"strand": true,
"transcript": "NM_002718.5",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1150,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6743,
"cdna_start": 1258,
"cds_end": null,
"cds_length": 3453,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000264977.8",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002718.5",
"protein_coding": true,
"protein_id": "ENSP00000264977.3",
"strand": true,
"transcript": "ENST00000264977.8",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1150,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6277,
"cdna_start": 1805,
"cds_end": null,
"cds_length": 3453,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000872859.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542918.1",
"strand": true,
"transcript": "ENST00000872859.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1150,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6041,
"cdna_start": 1569,
"cds_end": null,
"cds_length": 3453,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000872860.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542919.1",
"strand": true,
"transcript": "ENST00000872860.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1150,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4557,
"cdna_start": 1307,
"cds_end": null,
"cds_length": 3453,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000872863.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542922.1",
"strand": true,
"transcript": "ENST00000872863.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1150,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6832,
"cdna_start": 1349,
"cds_end": null,
"cds_length": 3453,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000930199.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600258.1",
"strand": true,
"transcript": "ENST00000930199.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1150,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6733,
"cdna_start": 1248,
"cds_end": null,
"cds_length": 3453,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000930200.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600259.1",
"strand": true,
"transcript": "ENST00000930200.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1121,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6707,
"cdna_start": 1311,
"cds_end": null,
"cds_length": 3366,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000930198.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600257.1",
"strand": true,
"transcript": "ENST00000930198.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1061,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5477,
"cdna_start": 1272,
"cds_end": null,
"cds_length": 3186,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000872861.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542920.1",
"strand": true,
"transcript": "ENST00000872861.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1061,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6549,
"cdna_start": 1331,
"cds_end": null,
"cds_length": 3186,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000930197.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600256.1",
"strand": true,
"transcript": "ENST00000930197.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1061,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6560,
"cdna_start": 1346,
"cds_end": null,
"cds_length": 3186,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000954297.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624356.1",
"strand": true,
"transcript": "ENST00000954297.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 992,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5518,
"cdna_start": 1520,
"cds_end": null,
"cds_length": 2979,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000872862.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542921.1",
"strand": true,
"transcript": "ENST00000872862.1",
"transcript_support_level": null
},
{
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"aa_ref": "C",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7252,
"cdna_start": 1767,
"cds_end": null,
"cds_length": 3453,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_006713686.5",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006713749.1",
"strand": true,
"transcript": "XM_006713686.5",
"transcript_support_level": null
},
{
"aa_alt": "C",
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"aa_length": 1150,
"aa_ref": "C",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7045,
"cdna_start": 1560,
"cds_end": null,
"cds_length": 3453,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_011512956.4",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011511258.1",
"strand": true,
"transcript": "XM_011512956.4",
"transcript_support_level": null
},
{
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"aa_ref": "C",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6476,
"cdna_start": 1258,
"cds_end": null,
"cds_length": 3186,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_017006787.3",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016862276.1",
"strand": true,
"transcript": "XM_017006787.3",
"transcript_support_level": null
},
{
"aa_alt": "C",
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"aa_length": 1061,
"aa_ref": "C",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6778,
"cdna_start": 1560,
"cds_end": null,
"cds_length": 3186,
"cds_start": 696,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047448509.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304465.1",
"strand": true,
"transcript": "XM_047448509.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
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"aa_ref": "C",
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"biotype": "protein_coding",
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"cdna_end": null,
"cdna_length": 6985,
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"cds_end": null,
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"cds_start": 696,
"consequences": [
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],
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"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047448510.1",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.696C>T",
"hgvs_p": "p.Cys232Cys",
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_047304466.1",
"strand": true,
"transcript": "XM_047448510.1",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"cdna_length": 4308,
"cdna_start": null,
"cds_end": null,
"cds_length": 1245,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001190447.2",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.-213-24638C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001177376.1",
"strand": true,
"transcript": "NM_001190447.2",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1782,
"cdna_start": null,
"cds_end": null,
"cds_length": 1245,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000490467.5",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "c.-213-24638C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419344.1",
"strand": true,
"transcript": "ENST00000490467.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3390,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XR_001740196.3",
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"hgvs_c": "n.1258C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_001740196.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs34629706",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0739056,
"gene_hgnc_id": 9307,
"gene_symbol": "PPP2R3A",
"gnomad_exomes_ac": 110048,
"gnomad_exomes_af": 0.0753195,
"gnomad_exomes_homalt": 4880,
"gnomad_genomes_ac": 9178,
"gnomad_genomes_af": 0.0603268,
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"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 5285,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "PPP2R3A-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.221,
"pos": 136002194,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002718.5"
}
]
}