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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: 14-74855280-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=74855280&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PROX2",
"hgnc_id": 26715,
"hgvs_c": "c.1631T>C",
"hgvs_p": "p.Ile544Thr",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_001243007.2",
"verdict": "Uncertain_significance"
},
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "YLPM1",
"hgnc_id": 17798,
"hgvs_c": "c.268A>G",
"hgvs_p": "p.Ile90Val",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 1,
"transcript": "ENST00000554107.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_score": 1,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": 0.1314,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.16,
"chr": "14",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.31673604249954224,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 592,
"aa_ref": "I",
"aa_start": 544,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4438,
"cdna_start": 2191,
"cds_end": null,
"cds_length": 1779,
"cds_start": 1631,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001243007.2",
"gene_hgnc_id": 26715,
"gene_symbol": "PROX2",
"hgvs_c": "c.1631T>C",
"hgvs_p": "p.Ile544Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000556489.4",
"protein_coding": true,
"protein_id": "NP_001229936.1",
"strand": false,
"transcript": "NM_001243007.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 592,
"aa_ref": "I",
"aa_start": 544,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4438,
"cdna_start": 2191,
"cds_end": null,
"cds_length": 1779,
"cds_start": 1631,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000556489.4",
"gene_hgnc_id": 26715,
"gene_symbol": "PROX2",
"hgvs_c": "c.1631T>C",
"hgvs_p": "p.Ile544Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001243007.2",
"protein_coding": true,
"protein_id": "ENSP00000451223.2",
"strand": false,
"transcript": "ENST00000556489.4",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 592,
"aa_ref": "I",
"aa_start": 544,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4515,
"cdna_start": 2268,
"cds_end": null,
"cds_length": 1779,
"cds_start": 1631,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001384314.1",
"gene_hgnc_id": 26715,
"gene_symbol": "PROX2",
"hgvs_c": "c.1631T>C",
"hgvs_p": "p.Ile544Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001371243.1",
"strand": false,
"transcript": "NM_001384314.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 365,
"aa_ref": "I",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3757,
"cdna_start": 1510,
"cds_end": null,
"cds_length": 1098,
"cds_start": 950,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001080408.3",
"gene_hgnc_id": 26715,
"gene_symbol": "PROX2",
"hgvs_c": "c.950T>C",
"hgvs_p": "p.Ile317Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001073877.2",
"strand": false,
"transcript": "NM_001080408.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 365,
"aa_ref": "I",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3928,
"cdna_start": 1519,
"cds_end": null,
"cds_length": 1098,
"cds_start": 950,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000673765.1",
"gene_hgnc_id": 26715,
"gene_symbol": "PROX2",
"hgvs_c": "c.950T>C",
"hgvs_p": "p.Ile317Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501015.1",
"strand": false,
"transcript": "ENST00000673765.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 109,
"aa_ref": "I",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4424,
"cdna_start": 269,
"cds_end": null,
"cds_length": 330,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000554107.2",
"gene_hgnc_id": 17798,
"gene_symbol": "YLPM1",
"hgvs_c": "c.268A>G",
"hgvs_p": "p.Ile90Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000476212.1",
"strand": true,
"transcript": "ENST00000554107.2",
"transcript_support_level": 3
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 592,
"aa_ref": "I",
"aa_start": 544,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2227,
"cdna_start": 1708,
"cds_end": null,
"cds_length": 1779,
"cds_start": 1631,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_005267543.5",
"gene_hgnc_id": 26715,
"gene_symbol": "PROX2",
"hgvs_c": "c.1631T>C",
"hgvs_p": "p.Ile544Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005267600.1",
"strand": false,
"transcript": "XM_005267543.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 696,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000553381.1",
"gene_hgnc_id": 17798,
"gene_symbol": "YLPM1",
"hgvs_c": "n.301A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000553381.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4503,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NR_169190.1",
"gene_hgnc_id": 26715,
"gene_symbol": "PROX2",
"hgvs_c": "n.2256T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_169190.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs762654328",
"effect": "missense_variant",
"frequency_reference_population": 0.00000385206,
"gene_hgnc_id": 26715,
"gene_symbol": "PROX2",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.00000284617,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131396,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.508,
"pos": 74855280,
"ref": "A",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.369,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001243007.2"
}
]
}