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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: 9-120862612-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=120862612&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 120862612,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000373896.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1106G>C",
"hgvs_p": "p.Arg369Pro",
"transcript": "NM_015651.3",
"protein_id": "NP_056466.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 580,
"cds_start": 1106,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1219,
"cdna_end": null,
"cdna_length": 4149,
"mane_select": "ENST00000373896.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1106G>C",
"hgvs_p": "p.Arg369Pro",
"transcript": "ENST00000373896.8",
"protein_id": "ENSP00000363003.3",
"transcript_support_level": 2,
"aa_start": 369,
"aa_end": null,
"aa_length": 580,
"cds_start": 1106,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1219,
"cdna_end": null,
"cdna_length": 4149,
"mane_select": "NM_015651.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1163G>C",
"hgvs_p": "p.Arg388Pro",
"transcript": "ENST00000616568.5",
"protein_id": "ENSP00000483946.1",
"transcript_support_level": 1,
"aa_start": 388,
"aa_end": null,
"aa_length": 599,
"cds_start": 1163,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1230,
"cdna_end": null,
"cdna_length": 4113,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "n.529G>C",
"hgvs_p": null,
"transcript": "ENST00000487555.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1163G>C",
"hgvs_p": "p.Arg388Pro",
"transcript": "NM_001286840.1",
"protein_id": "NP_001273769.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 599,
"cds_start": 1163,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1230,
"cdna_end": null,
"cdna_length": 4160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.479G>C",
"hgvs_p": "p.Arg160Pro",
"transcript": "NM_001286842.1",
"protein_id": "NP_001273771.1",
"transcript_support_level": null,
"aa_start": 160,
"aa_end": null,
"aa_length": 371,
"cds_start": 479,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 3526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.479G>C",
"hgvs_p": "p.Arg160Pro",
"transcript": "ENST00000419155.5",
"protein_id": "ENSP00000407433.1",
"transcript_support_level": 2,
"aa_start": 160,
"aa_end": null,
"aa_length": 371,
"cds_start": 479,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 3525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.479G>C",
"hgvs_p": "p.Arg160Pro",
"transcript": "ENST00000453868.5",
"protein_id": "ENSP00000395938.1",
"transcript_support_level": 5,
"aa_start": 160,
"aa_end": null,
"aa_length": 172,
"cds_start": 479,
"cds_end": null,
"cds_length": 521,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1283G>C",
"hgvs_p": "p.Arg428Pro",
"transcript": "XM_005251906.4",
"protein_id": "XP_005251963.2",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 639,
"cds_start": 1283,
"cds_end": null,
"cds_length": 1920,
"cdna_start": 1329,
"cdna_end": null,
"cdna_length": 4259,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1106G>C",
"hgvs_p": "p.Arg369Pro",
"transcript": "XM_011518509.4",
"protein_id": "XP_011516811.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 580,
"cds_start": 1106,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1603,
"cdna_end": null,
"cdna_length": 4533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1106G>C",
"hgvs_p": "p.Arg369Pro",
"transcript": "XM_017014612.3",
"protein_id": "XP_016870101.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 580,
"cds_start": 1106,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 3360,
"cdna_end": null,
"cdna_length": 6290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1163G>C",
"hgvs_p": "p.Arg388Pro",
"transcript": "XM_011518515.3",
"protein_id": "XP_011516817.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 422,
"cds_start": 1163,
"cds_end": null,
"cds_length": 1269,
"cdna_start": 1230,
"cdna_end": null,
"cdna_length": 1439,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.587G>C",
"hgvs_p": "p.Arg196Pro",
"transcript": "XM_024447507.2",
"protein_id": "XP_024303275.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 407,
"cds_start": 587,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 661,
"cdna_end": null,
"cdna_length": 3591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.587G>C",
"hgvs_p": "p.Arg196Pro",
"transcript": "XM_047423211.1",
"protein_id": "XP_047279167.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 407,
"cds_start": 587,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 1070,
"cdna_end": null,
"cdna_length": 4000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "n.266G>C",
"hgvs_p": null,
"transcript": "ENST00000464712.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "n.596G>C",
"hgvs_p": null,
"transcript": "NR_104601.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "n.414+1G>C",
"hgvs_p": null,
"transcript": "ENST00000467266.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1162+1G>C",
"hgvs_p": null,
"transcript": "XM_047423210.1",
"protein_id": "XP_047279166.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 443,
"cds_start": -4,
"cds_end": null,
"cds_length": 1332,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1162+1G>C",
"hgvs_p": null,
"transcript": "XM_011518516.3",
"protein_id": "XP_011516818.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 388,
"cds_start": -4,
"cds_end": null,
"cds_length": 1167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1316,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"dbsnp": "rs150134029",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07361513376235962,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.085,
"revel_prediction": "Benign",
"alphamissense_score": 0.201,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.576,
"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": "ENST00000373896.8",
"gene_symbol": "PHF19",
"hgnc_id": 24566,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1106G>C",
"hgvs_p": "p.Arg369Pro"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}