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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: 9-136434050-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=136434050&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 136434050,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_019892.6",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "NM_019892.6",
"protein_id": "NP_063945.2",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 644,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000371712.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019892.6"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000371712.4",
"protein_id": "ENSP00000360777.3",
"transcript_support_level": 1,
"aa_start": 341,
"aa_end": null,
"aa_length": 644,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_019892.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371712.4"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1042G>A",
"hgvs_p": "p.Gly348Ser",
"transcript": "ENST00000930360.1",
"protein_id": "ENSP00000600419.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 651,
"cds_start": 1042,
"cds_end": null,
"cds_length": 1956,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930360.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "NM_001318502.2",
"protein_id": "NP_001305431.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 643,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1932,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318502.2"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000910890.1",
"protein_id": "ENSP00000580949.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 643,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1932,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910890.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1018G>A",
"hgvs_p": "p.Gly340Ser",
"transcript": "ENST00000960334.1",
"protein_id": "ENSP00000630393.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 643,
"cds_start": 1018,
"cds_end": null,
"cds_length": 1932,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960334.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000960335.1",
"protein_id": "ENSP00000630394.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 630,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960335.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000930359.1",
"protein_id": "ENSP00000600418.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 629,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930359.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000676019.1",
"protein_id": "ENSP00000501984.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 610,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676019.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000910891.1",
"protein_id": "ENSP00000580950.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 609,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910891.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000910889.1",
"protein_id": "ENSP00000580948.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 608,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1827,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910889.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000930358.1",
"protein_id": "ENSP00000600417.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 604,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1815,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930358.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000960337.1",
"protein_id": "ENSP00000630396.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 603,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1812,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960337.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.250G>A",
"hgvs_p": "p.Gly84Ser",
"transcript": "ENST00000675256.1",
"protein_id": "ENSP00000502517.1",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 86,
"cds_start": 250,
"cds_end": null,
"cds_length": 263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675256.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "XM_017014926.2",
"protein_id": "XP_016870415.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 602,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1809,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017014926.2"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "XM_047423603.1",
"protein_id": "XP_047279559.1",
"transcript_support_level": null,
"aa_start": 341,
"aa_end": null,
"aa_length": 601,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1806,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423603.1"
},
{
"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": 10,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.998+23G>A",
"hgvs_p": null,
"transcript": "ENST00000930356.1",
"protein_id": "ENSP00000600415.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 632,
"cds_start": null,
"cds_end": null,
"cds_length": 1899,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930356.1"
},
{
"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": 10,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.998+23G>A",
"hgvs_p": null,
"transcript": "ENST00000930357.1",
"protein_id": "ENSP00000600416.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 631,
"cds_start": null,
"cds_end": null,
"cds_length": 1896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930357.1"
},
{
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.813-771G>A",
"hgvs_p": null,
"transcript": "ENST00000960336.1",
"protein_id": "ENSP00000630395.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 570,
"cds_start": null,
"cds_end": null,
"cds_length": 1713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960336.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "n.292G>A",
"hgvs_p": null,
"transcript": "ENST00000674513.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000674513.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "n.1447G>A",
"hgvs_p": null,
"transcript": "XR_929828.3",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "XR_929828.3"
}
],
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"dbsnp": "rs780882740",
"frequency_reference_population": 0.000015104289,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000151043,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7271808385848999,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.54,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3432,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.198,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_019892.6",
"gene_symbol": "INPP5E",
"hgnc_id": 21474,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser"
}
],
"clinvar_disease": "Joubert syndrome,Joubert syndrome 1,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 US:1",
"phenotype_combined": "Joubert syndrome|Joubert syndrome 1|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}