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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: 9-92415330-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=92415330&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "OMD",
"hgnc_id": 8134,
"hgvs_c": "c.1088G>T",
"hgvs_p": "p.Gly363Val",
"inheritance_mode": "",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_005014.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"intron_variant"
],
"gene_symbol": "CENPP",
"hgnc_id": 32933,
"hgvs_c": "c.564+35471C>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_001012267.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 0,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9657,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.16,
"chr": "9",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8351879715919495,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 421,
"aa_ref": "G",
"aa_start": 363,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4324,
"cdna_start": 1374,
"cds_end": null,
"cds_length": 1266,
"cds_start": 1088,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_005014.3",
"gene_hgnc_id": 8134,
"gene_symbol": "OMD",
"hgvs_c": "c.1088G>T",
"hgvs_p": "p.Gly363Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000375550.5",
"protein_coding": true,
"protein_id": "NP_005005.1",
"strand": false,
"transcript": "NM_005014.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 421,
"aa_ref": "G",
"aa_start": 363,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4324,
"cdna_start": 1374,
"cds_end": null,
"cds_length": 1266,
"cds_start": 1088,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000375550.5",
"gene_hgnc_id": 8134,
"gene_symbol": "OMD",
"hgvs_c": "c.1088G>T",
"hgvs_p": "p.Gly363Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005014.3",
"protein_coding": true,
"protein_id": "ENSP00000364700.4",
"strand": false,
"transcript": "ENST00000375550.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 288,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8293,
"cdna_start": null,
"cds_end": null,
"cds_length": 867,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001012267.3",
"gene_hgnc_id": 32933,
"gene_symbol": "CENPP",
"hgvs_c": "c.564+35471C>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000375587.8",
"protein_coding": true,
"protein_id": "NP_001012267.1",
"strand": true,
"transcript": "NM_001012267.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 288,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8293,
"cdna_start": null,
"cds_end": null,
"cds_length": 867,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000375587.8",
"gene_hgnc_id": 32933,
"gene_symbol": "CENPP",
"hgvs_c": "c.564+35471C>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001012267.3",
"protein_coding": true,
"protein_id": "ENSP00000364737.3",
"strand": true,
"transcript": "ENST00000375587.8",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 242,
"aa_ref": "G",
"aa_start": 184,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3152,
"cdna_start": 827,
"cds_end": null,
"cds_length": 729,
"cds_start": 551,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000949678.1",
"gene_hgnc_id": 8134,
"gene_symbol": "OMD",
"hgvs_c": "c.551G>T",
"hgvs_p": "p.Gly184Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619737.1",
"strand": false,
"transcript": "ENST00000949678.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 176,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3231,
"cdna_start": null,
"cds_end": null,
"cds_length": 531,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001286969.1",
"gene_hgnc_id": 32933,
"gene_symbol": "CENPP",
"hgvs_c": "c.228+35471C>A",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001273898.1",
"strand": true,
"transcript": "NM_001286969.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 196,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8268,
"cdna_start": null,
"cds_end": null,
"cds_length": 591,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024447543.2",
"gene_hgnc_id": 32933,
"gene_symbol": "CENPP",
"hgvs_c": "c.288+35471C>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024303311.1",
"strand": true,
"transcript": "XM_024447543.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 192,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 920,
"cdna_start": null,
"cds_end": null,
"cds_length": 579,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011518689.2",
"gene_hgnc_id": 32933,
"gene_symbol": "CENPP",
"hgvs_c": "c.564+35471C>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011516991.1",
"strand": true,
"transcript": "XM_011518689.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1304449123",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 8134,
"gene_symbol": "OMD",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.298,
"pos": 92415330,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.362,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005014.3"
}
]
}