← Back to variant description
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: 9-120858047-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=120858047&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 120858047,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000373896.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1640G>A",
"hgvs_p": "p.Gly547Glu",
"transcript": "NM_015651.3",
"protein_id": "NP_056466.1",
"transcript_support_level": null,
"aa_start": 547,
"aa_end": null,
"aa_length": 580,
"cds_start": 1640,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1753,
"cdna_end": null,
"cdna_length": 4149,
"mane_select": "ENST00000373896.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1640G>A",
"hgvs_p": "p.Gly547Glu",
"transcript": "ENST00000373896.8",
"protein_id": "ENSP00000363003.3",
"transcript_support_level": 2,
"aa_start": 547,
"aa_end": null,
"aa_length": 580,
"cds_start": 1640,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1753,
"cdna_end": null,
"cdna_length": 4149,
"mane_select": "NM_015651.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1697G>A",
"hgvs_p": "p.Gly566Glu",
"transcript": "ENST00000616568.5",
"protein_id": "ENSP00000483946.1",
"transcript_support_level": 1,
"aa_start": 566,
"aa_end": null,
"aa_length": 599,
"cds_start": 1697,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1764,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "n.975G>A",
"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": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1697G>A",
"hgvs_p": "p.Gly566Glu",
"transcript": "NM_001286840.1",
"protein_id": "NP_001273769.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 599,
"cds_start": 1697,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1764,
"cdna_end": null,
"cdna_length": 4160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1013G>A",
"hgvs_p": "p.Gly338Glu",
"transcript": "NM_001286842.1",
"protein_id": "NP_001273771.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 371,
"cds_start": 1013,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 3526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1013G>A",
"hgvs_p": "p.Gly338Glu",
"transcript": "ENST00000419155.5",
"protein_id": "ENSP00000407433.1",
"transcript_support_level": 2,
"aa_start": 338,
"aa_end": null,
"aa_length": 371,
"cds_start": 1013,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 3525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1817G>A",
"hgvs_p": "p.Gly606Glu",
"transcript": "XM_005251906.4",
"protein_id": "XP_005251963.2",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 639,
"cds_start": 1817,
"cds_end": null,
"cds_length": 1920,
"cdna_start": 1863,
"cdna_end": null,
"cdna_length": 4259,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1640G>A",
"hgvs_p": "p.Gly547Glu",
"transcript": "XM_011518509.4",
"protein_id": "XP_011516811.1",
"transcript_support_level": null,
"aa_start": 547,
"aa_end": null,
"aa_length": 580,
"cds_start": 1640,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 2137,
"cdna_end": null,
"cdna_length": 4533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1640G>A",
"hgvs_p": "p.Gly547Glu",
"transcript": "XM_017014612.3",
"protein_id": "XP_016870101.1",
"transcript_support_level": null,
"aa_start": 547,
"aa_end": null,
"aa_length": 580,
"cds_start": 1640,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 3894,
"cdna_end": null,
"cdna_length": 6290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1121G>A",
"hgvs_p": "p.Gly374Glu",
"transcript": "XM_024447507.2",
"protein_id": "XP_024303275.1",
"transcript_support_level": null,
"aa_start": 374,
"aa_end": null,
"aa_length": 407,
"cds_start": 1121,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 1195,
"cdna_end": null,
"cdna_length": 3591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "c.1121G>A",
"hgvs_p": "p.Gly374Glu",
"transcript": "XM_047423211.1",
"protein_id": "XP_047279167.1",
"transcript_support_level": null,
"aa_start": 374,
"aa_end": null,
"aa_length": 407,
"cds_start": 1121,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 1604,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "n.1042G>A",
"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": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"hgvs_c": "n.*147G>A",
"hgvs_p": null,
"transcript": "ENST00000462229.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHF19",
"gene_hgnc_id": 24566,
"dbsnp": "rs2045398598",
"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": 0.693335235118866,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.387,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8956,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.006,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000373896.8",
"gene_symbol": "PHF19",
"hgnc_id": 24566,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1640G>A",
"hgvs_p": "p.Gly547Glu"
}
],
"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
}