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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: 9-120869233-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=120869233&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 120869233,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_015651.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.563C>T",
"hgvs_p": "p.Pro188Leu",
"transcript": "NM_015651.3",
"protein_id": "NP_056466.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 580,
"cds_start": 563,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 676,
"cdna_end": null,
"cdna_length": 4149,
"mane_select": "ENST00000373896.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.563C>T",
"hgvs_p": "p.Pro188Leu",
"transcript": "ENST00000373896.8",
"protein_id": "ENSP00000363003.3",
"transcript_support_level": 2,
"aa_start": 188,
"aa_end": null,
"aa_length": 580,
"cds_start": 563,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 676,
"cdna_end": null,
"cdna_length": 4149,
"mane_select": "NM_015651.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.620C>T",
"hgvs_p": "p.Pro207Leu",
"transcript": "ENST00000616568.5",
"protein_id": "ENSP00000483946.1",
"transcript_support_level": 1,
"aa_start": 207,
"aa_end": null,
"aa_length": 599,
"cds_start": 620,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 4113,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.620C>T",
"hgvs_p": "p.Pro207Leu",
"transcript": "NM_001286840.1",
"protein_id": "NP_001273769.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 599,
"cds_start": 620,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 4160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.740C>T",
"hgvs_p": "p.Pro247Leu",
"transcript": "XM_005251906.4",
"protein_id": "XP_005251963.2",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 639,
"cds_start": 740,
"cds_end": null,
"cds_length": 1920,
"cdna_start": 786,
"cdna_end": null,
"cdna_length": 4259,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.563C>T",
"hgvs_p": "p.Pro188Leu",
"transcript": "XM_011518509.4",
"protein_id": "XP_011516811.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 580,
"cds_start": 563,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1060,
"cdna_end": null,
"cdna_length": 4533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.563C>T",
"hgvs_p": "p.Pro188Leu",
"transcript": "XM_017014612.3",
"protein_id": "XP_016870101.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 580,
"cds_start": 563,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 2817,
"cdna_end": null,
"cdna_length": 6290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.620C>T",
"hgvs_p": "p.Pro207Leu",
"transcript": "XM_047423210.1",
"protein_id": "XP_047279166.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 443,
"cds_start": 620,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 1502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.620C>T",
"hgvs_p": "p.Pro207Leu",
"transcript": "XM_011518515.3",
"protein_id": "XP_011516817.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 422,
"cds_start": 620,
"cds_end": null,
"cds_length": 1269,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 1439,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.44C>T",
"hgvs_p": "p.Pro15Leu",
"transcript": "XM_024447507.2",
"protein_id": "XP_024303275.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 407,
"cds_start": 44,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 118,
"cdna_end": null,
"cdna_length": 3591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.44C>T",
"hgvs_p": "p.Pro15Leu",
"transcript": "XM_047423211.1",
"protein_id": "XP_047279167.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 407,
"cds_start": 44,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 527,
"cdna_end": null,
"cdna_length": 4000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.620C>T",
"hgvs_p": "p.Pro207Leu",
"transcript": "XM_011518516.3",
"protein_id": "XP_011516818.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 388,
"cds_start": 620,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 1316,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.*66C>T",
"hgvs_p": null,
"transcript": "ENST00000436309.5",
"protein_id": "ENSP00000408479.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 164,
"cds_start": -4,
"cds_end": null,
"cds_length": 497,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"dbsnp": "rs1287749636",
"frequency_reference_population": 0.0000012405517,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.84955e-7,
"gnomad_genomes_af": 0.00000656875,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.13995841145515442,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.18,
"revel_prediction": "Benign",
"alphamissense_score": 0.1089,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.514,
"phylop100way_prediction": "Benign",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_015651.3",
"gene_symbol": "PHF19",
"hgnc_id": 24566,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.563C>T",
"hgvs_p": "p.Pro188Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}