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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: 9-136429731-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=136429731&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"effects": [
"stop_gained"
],
"gene_symbol": "INPP5E",
"hgnc_id": 21474,
"hgvs_c": "c.1879C>T",
"hgvs_p": "p.Gln627*",
"inheritance_mode": "AR",
"pathogenic_score": 8,
"score": 8,
"transcript": "NM_019892.6",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
"acmg_score": 8,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.62,
"chr": "9",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Joubert syndrome 1,MORM syndrome",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6200000047683716,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 644,
"aa_ref": "Q",
"aa_start": 627,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3417,
"cdna_start": 2305,
"cds_end": null,
"cds_length": 1935,
"cds_start": 1879,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_019892.6",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1879C>T",
"hgvs_p": "p.Gln627*",
"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": "*",
"aa_end": null,
"aa_length": 644,
"aa_ref": "Q",
"aa_start": 627,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3417,
"cdna_start": 2305,
"cds_end": null,
"cds_length": 1935,
"cds_start": 1879,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000371712.4",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1879C>T",
"hgvs_p": "p.Gln627*",
"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": "*",
"aa_end": null,
"aa_length": 651,
"aa_ref": "Q",
"aa_start": 634,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3389,
"cdna_start": 2283,
"cds_end": null,
"cds_length": 1956,
"cds_start": 1900,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000930360.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1900C>T",
"hgvs_p": "p.Gln634*",
"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": "*",
"aa_end": null,
"aa_length": 643,
"aa_ref": "Q",
"aa_start": 626,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3414,
"cdna_start": 2302,
"cds_end": null,
"cds_length": 1932,
"cds_start": 1876,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001318502.2",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1876C>T",
"hgvs_p": "p.Gln626*",
"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": "*",
"aa_end": null,
"aa_length": 643,
"aa_ref": "Q",
"aa_start": 626,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3440,
"cdna_start": 2328,
"cds_end": null,
"cds_length": 1932,
"cds_start": 1876,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910890.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1876C>T",
"hgvs_p": "p.Gln626*",
"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": "*",
"aa_end": null,
"aa_length": 643,
"aa_ref": "Q",
"aa_start": 626,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3430,
"cdna_start": 2318,
"cds_end": null,
"cds_length": 1932,
"cds_start": 1876,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000960334.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1876C>T",
"hgvs_p": "p.Gln626*",
"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": "*",
"aa_end": null,
"aa_length": 632,
"aa_ref": "Q",
"aa_start": 615,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3380,
"cdna_start": 2268,
"cds_end": null,
"cds_length": 1899,
"cds_start": 1843,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000930356.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1843C>T",
"hgvs_p": "p.Gln615*",
"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": "*",
"aa_end": null,
"aa_length": 631,
"aa_ref": "Q",
"aa_start": 614,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3375,
"cdna_start": 2263,
"cds_end": null,
"cds_length": 1896,
"cds_start": 1840,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000930357.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1840C>T",
"hgvs_p": "p.Gln614*",
"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": "*",
"aa_end": null,
"aa_length": 630,
"aa_ref": "Q",
"aa_start": 613,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3383,
"cdna_start": 2275,
"cds_end": null,
"cds_length": 1893,
"cds_start": 1837,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000960335.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1837C>T",
"hgvs_p": "p.Gln613*",
"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": "*",
"aa_end": null,
"aa_length": 629,
"aa_ref": "Q",
"aa_start": 612,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3347,
"cdna_start": 2234,
"cds_end": null,
"cds_length": 1890,
"cds_start": 1834,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000930359.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1834C>T",
"hgvs_p": "p.Gln612*",
"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": "*",
"aa_end": null,
"aa_length": 610,
"aa_ref": "Q",
"aa_start": 593,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3315,
"cdna_start": 2203,
"cds_end": null,
"cds_length": 1833,
"cds_start": 1777,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000676019.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1777C>T",
"hgvs_p": "p.Gln593*",
"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": "*",
"aa_end": null,
"aa_length": 609,
"aa_ref": "Q",
"aa_start": 592,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3331,
"cdna_start": 2219,
"cds_end": null,
"cds_length": 1830,
"cds_start": 1774,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000910891.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1774C>T",
"hgvs_p": "p.Gln592*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580950.1",
"strand": false,
"transcript": "ENST00000910891.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 608,
"aa_ref": "Q",
"aa_start": 591,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3341,
"cdna_start": 2234,
"cds_end": null,
"cds_length": 1827,
"cds_start": 1771,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000910889.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1771C>T",
"hgvs_p": "p.Gln591*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580948.1",
"strand": false,
"transcript": "ENST00000910889.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 604,
"aa_ref": "Q",
"aa_start": 587,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3285,
"cdna_start": 2173,
"cds_end": null,
"cds_length": 1815,
"cds_start": 1759,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000930358.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1759C>T",
"hgvs_p": "p.Gln587*",
"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": "*",
"aa_end": null,
"aa_length": 603,
"aa_ref": "Q",
"aa_start": 586,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3280,
"cdna_start": 2173,
"cds_end": null,
"cds_length": 1812,
"cds_start": 1756,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000960337.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.Gln586*",
"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": "*",
"aa_end": null,
"aa_length": 570,
"aa_ref": "Q",
"aa_start": 553,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3188,
"cdna_start": 2080,
"cds_end": null,
"cds_length": 1713,
"cds_start": 1657,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000960336.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.1657C>T",
"hgvs_p": "p.Gln553*",
"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": null,
"aa_end": null,
"aa_length": 602,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3370,
"cdna_start": null,
"cds_end": null,
"cds_length": 1809,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_017014926.2",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.*23C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016870415.1",
"strand": false,
"transcript": "XM_017014926.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 601,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3367,
"cdna_start": null,
"cds_end": null,
"cds_length": 1806,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047423603.1",
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"hgvs_c": "c.*23C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279559.1",
"strand": false,
"transcript": "XM_047423603.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs121918127",
"effect": "stop_gained",
"frequency_reference_population": null,
"gene_hgnc_id": 21474,
"gene_symbol": "INPP5E",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "MORM syndrome|MORM syndrome;Joubert syndrome 1",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.488,
"pos": 136429731,
"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"
}
]
}