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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: 9-136439387-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=136439387&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "INPP5E",
"hgnc_id": 21474,
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_019892.6",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_score": -21,
"allele_count_reference_population": 6678,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.86,
"chr": "9",
"clinvar_classification": "Benign",
"clinvar_disease": "Joubert syndrome,Joubert syndrome 1,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8600000143051147,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 644,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3417,
"cdna_start": 459,
"cds_end": null,
"cds_length": 1935,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_019892.6",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000371712.4",
"protein_coding": true,
"protein_id": "NP_063945.2",
"strand": false,
"transcript": "NM_019892.6",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 644,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3417,
"cdna_start": 459,
"cds_end": null,
"cds_length": 1935,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000371712.4",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_019892.6",
"protein_coding": true,
"protein_id": "ENSP00000360777.3",
"strand": false,
"transcript": "ENST00000371712.4",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 651,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3389,
"cdna_start": 416,
"cds_end": null,
"cds_length": 1956,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000930360.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600419.1",
"strand": false,
"transcript": "ENST00000930360.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 643,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3414,
"cdna_start": 459,
"cds_end": null,
"cds_length": 1932,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001318502.2",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305431.1",
"strand": false,
"transcript": "NM_001318502.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 643,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3440,
"cdna_start": 485,
"cds_end": null,
"cds_length": 1932,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000910890.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580949.1",
"strand": false,
"transcript": "ENST00000910890.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 643,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3430,
"cdna_start": 475,
"cds_end": null,
"cds_length": 1932,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000960334.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000630393.1",
"strand": false,
"transcript": "ENST00000960334.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 632,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3380,
"cdna_start": 458,
"cds_end": null,
"cds_length": 1899,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000930356.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600415.1",
"strand": false,
"transcript": "ENST00000930356.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 631,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3375,
"cdna_start": 456,
"cds_end": null,
"cds_length": 1896,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000930357.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600416.1",
"strand": false,
"transcript": "ENST00000930357.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 630,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3383,
"cdna_start": 471,
"cds_end": null,
"cds_length": 1893,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000960335.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000630394.1",
"strand": false,
"transcript": "ENST00000960335.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 629,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3347,
"cdna_start": 433,
"cds_end": null,
"cds_length": 1890,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000930359.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600418.1",
"strand": false,
"transcript": "ENST00000930359.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 610,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3315,
"cdna_start": 459,
"cds_end": null,
"cds_length": 1833,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000676019.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501984.1",
"strand": false,
"transcript": "ENST00000676019.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 609,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3331,
"cdna_start": 478,
"cds_end": null,
"cds_length": 1830,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000910891.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580950.1",
"strand": false,
"transcript": "ENST00000910891.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
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"aa_length": 608,
"aa_ref": "S",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3341,
"cdna_start": 496,
"cds_end": null,
"cds_length": 1827,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 1,
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"feature": "ENST00000910889.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580948.1",
"strand": false,
"transcript": "ENST00000910889.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
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"aa_length": 604,
"aa_ref": "S",
"aa_start": 11,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3285,
"cdna_start": 447,
"cds_end": null,
"cds_length": 1815,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000930358.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600417.1",
"strand": false,
"transcript": "ENST00000930358.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
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"aa_length": 603,
"aa_ref": "S",
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"biotype": "protein_coding",
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"cdna_end": null,
"cdna_length": 3280,
"cdna_start": 450,
"cds_end": null,
"cds_length": 1812,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000960337.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000630396.1",
"strand": false,
"transcript": "ENST00000960337.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 570,
"aa_ref": "S",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3188,
"cdna_start": 456,
"cds_end": null,
"cds_length": 1713,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000960336.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000630395.1",
"strand": false,
"transcript": "ENST00000960336.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 602,
"aa_ref": "S",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3370,
"cdna_start": 459,
"cds_end": null,
"cds_length": 1809,
"cds_start": 33,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_017014926.2",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_016870415.1",
"strand": false,
"transcript": "XM_017014926.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
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"aa_ref": "S",
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"cdna_start": 459,
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"cds_length": 1806,
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"consequences": [
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],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_047423603.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.33C>G",
"hgvs_p": "p.Ser11Ser",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279559.1",
"strand": false,
"transcript": "XM_047423603.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4311,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000635815.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "n.437C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000635815.1",
"transcript_support_level": 6
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2066,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XR_929828.3",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "n.459C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_929828.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs79161998",
"effect": "synonymous_variant",
"frequency_reference_population": 0.004562697,
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"gnomad_exomes_ac": 3200,
"gnomad_exomes_af": 0.00243999,
"gnomad_exomes_homalt": 104,
"gnomad_genomes_ac": 3478,
"gnomad_genomes_af": 0.0228623,
"gnomad_genomes_homalt": 168,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 272,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Joubert syndrome|Joubert syndrome 1|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -3.435,
"pos": 136439387,
"ref": "G",
"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_019892.6"
}
]
}