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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: 9-93673799-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=93673799&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 93673799,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_005392.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2563G>A",
"hgvs_p": "p.Asp855Asn",
"transcript": "NM_005392.4",
"protein_id": "NP_005383.3",
"transcript_support_level": null,
"aa_start": 855,
"aa_end": null,
"aa_length": 1096,
"cds_start": 2563,
"cds_end": null,
"cds_length": 3291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000359246.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005392.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2563G>A",
"hgvs_p": "p.Asp855Asn",
"transcript": "ENST00000359246.9",
"protein_id": "ENSP00000352185.4",
"transcript_support_level": 1,
"aa_start": 855,
"aa_end": null,
"aa_length": 1096,
"cds_start": 2563,
"cds_end": null,
"cds_length": 3291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005392.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000359246.9"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2566G>A",
"hgvs_p": "p.Asp856Asn",
"transcript": "ENST00000851896.1",
"protein_id": "ENSP00000521955.1",
"transcript_support_level": null,
"aa_start": 856,
"aa_end": null,
"aa_length": 1097,
"cds_start": 2566,
"cds_end": null,
"cds_length": 3294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851896.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2566G>A",
"hgvs_p": "p.Asp856Asn",
"transcript": "ENST00000937581.1",
"protein_id": "ENSP00000607640.1",
"transcript_support_level": null,
"aa_start": 856,
"aa_end": null,
"aa_length": 1096,
"cds_start": 2566,
"cds_end": null,
"cds_length": 3291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937581.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2476G>A",
"hgvs_p": "p.Asp826Asn",
"transcript": "ENST00000942581.1",
"protein_id": "ENSP00000612640.1",
"transcript_support_level": null,
"aa_start": 826,
"aa_end": null,
"aa_length": 1067,
"cds_start": 2476,
"cds_end": null,
"cds_length": 3204,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942581.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2473G>A",
"hgvs_p": "p.Asp825Asn",
"transcript": "ENST00000851898.1",
"protein_id": "ENSP00000521957.1",
"transcript_support_level": null,
"aa_start": 825,
"aa_end": null,
"aa_length": 1066,
"cds_start": 2473,
"cds_end": null,
"cds_length": 3201,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851898.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2461G>A",
"hgvs_p": "p.Asp821Asn",
"transcript": "ENST00000851897.1",
"protein_id": "ENSP00000521956.1",
"transcript_support_level": null,
"aa_start": 821,
"aa_end": null,
"aa_length": 1062,
"cds_start": 2461,
"cds_end": null,
"cds_length": 3189,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851897.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2395G>A",
"hgvs_p": "p.Asp799Asn",
"transcript": "ENST00000851899.1",
"protein_id": "ENSP00000521958.1",
"transcript_support_level": null,
"aa_start": 799,
"aa_end": null,
"aa_length": 1040,
"cds_start": 2395,
"cds_end": null,
"cds_length": 3123,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851899.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.259G>A",
"hgvs_p": "p.Asp87Asn",
"transcript": "ENST00000610682.1",
"protein_id": "ENSP00000479936.1",
"transcript_support_level": 5,
"aa_start": 87,
"aa_end": null,
"aa_length": 328,
"cds_start": 259,
"cds_end": null,
"cds_length": 987,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000610682.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2566G>A",
"hgvs_p": "p.Asp856Asn",
"transcript": "XM_005252051.3",
"protein_id": "XP_005252108.1",
"transcript_support_level": null,
"aa_start": 856,
"aa_end": null,
"aa_length": 1097,
"cds_start": 2566,
"cds_end": null,
"cds_length": 3294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005252051.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2557G>A",
"hgvs_p": "p.Asp853Asn",
"transcript": "XM_047423474.1",
"protein_id": "XP_047279430.1",
"transcript_support_level": null,
"aa_start": 853,
"aa_end": null,
"aa_length": 1094,
"cds_start": 2557,
"cds_end": null,
"cds_length": 3285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423474.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2461G>A",
"hgvs_p": "p.Asp821Asn",
"transcript": "XM_006717143.3",
"protein_id": "XP_006717206.1",
"transcript_support_level": null,
"aa_start": 821,
"aa_end": null,
"aa_length": 1062,
"cds_start": 2461,
"cds_end": null,
"cds_length": 3189,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006717143.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"hgvs_c": "c.2458G>A",
"hgvs_p": "p.Asp820Asn",
"transcript": "XM_047423475.1",
"protein_id": "XP_047279431.1",
"transcript_support_level": null,
"aa_start": 820,
"aa_end": null,
"aa_length": 1061,
"cds_start": 2458,
"cds_end": null,
"cds_length": 3186,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423475.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124902215",
"gene_hgnc_id": null,
"hgvs_c": "c.*694G>A",
"hgvs_p": null,
"transcript": "XM_047424311.1",
"protein_id": "XP_047280267.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 658,
"cds_start": null,
"cds_end": null,
"cds_length": 1977,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047424311.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124902215",
"gene_hgnc_id": null,
"hgvs_c": "c.*694G>A",
"hgvs_p": null,
"transcript": "XM_047424313.1",
"protein_id": "XP_047280269.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 646,
"cds_start": null,
"cds_end": null,
"cds_length": 1941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047424313.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124902215",
"gene_hgnc_id": null,
"hgvs_c": "c.*694G>A",
"hgvs_p": null,
"transcript": "XM_047424314.1",
"protein_id": "XP_047280270.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 646,
"cds_start": null,
"cds_end": null,
"cds_length": 1941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047424314.1"
}
],
"gene_symbol": "PHF2",
"gene_hgnc_id": 8920,
"dbsnp": "rs193921057",
"frequency_reference_population": 0.0002623871,
"hom_count_reference_population": 1,
"allele_count_reference_population": 423,
"gnomad_exomes_af": 0.000263726,
"gnomad_genomes_af": 0.000249547,
"gnomad_exomes_ac": 385,
"gnomad_genomes_ac": 38,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1444285809993744,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.169,
"revel_prediction": "Benign",
"alphamissense_score": 0.1189,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.634,
"phylop100way_prediction": "Pathogenic",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_005392.4",
"gene_symbol": "PHF2",
"hgnc_id": 8920,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2563G>A",
"hgvs_p": "p.Asp855Asn"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "XM_047424311.1",
"gene_symbol": "LOC124902215",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*694G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Prostate cancer,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Prostate cancer|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}