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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: 10-70435285-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=70435285&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1_Strong",
"PS3",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"splice_donor_variant",
"intron_variant"
],
"gene_symbol": "NODAL",
"hgnc_id": 7865,
"hgvs_c": "c.891+1G>A",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_018055.5",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000280401",
"hgnc_id": null,
"hgvs_c": "n.457C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 18,
"score": 18,
"transcript": "ENST00000624563.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PS3,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.34,
"chr": "10",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": " 5, autosomal, visceral,Heterotaxy,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.3400000035762787,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 347,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2058,
"cdna_start": null,
"cds_end": null,
"cds_length": 1044,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_018055.5",
"gene_hgnc_id": 7865,
"gene_symbol": "NODAL",
"hgvs_c": "c.891+1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000287139.8",
"protein_coding": true,
"protein_id": "NP_060525.3",
"strand": false,
"transcript": "NM_018055.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 347,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2058,
"cdna_start": null,
"cds_end": null,
"cds_length": 1044,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000287139.8",
"gene_hgnc_id": 7865,
"gene_symbol": "NODAL",
"hgvs_c": "c.891+1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018055.5",
"protein_coding": true,
"protein_id": "ENSP00000287139.3",
"strand": false,
"transcript": "ENST00000287139.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 292,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1066,
"cdna_start": null,
"cds_end": null,
"cds_length": 879,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000414871.1",
"gene_hgnc_id": 7865,
"gene_symbol": "NODAL",
"hgvs_c": "c.726+1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000394468.1",
"strand": false,
"transcript": "ENST00000414871.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 214,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1879,
"cdna_start": null,
"cds_end": null,
"cds_length": 645,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001329906.2",
"gene_hgnc_id": 7865,
"gene_symbol": "NODAL",
"hgvs_c": "c.492+1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001316835.1",
"strand": false,
"transcript": "NM_001329906.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 214,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1984,
"cdna_start": null,
"cds_end": null,
"cds_length": 645,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024448028.2",
"gene_hgnc_id": 7865,
"gene_symbol": "NODAL",
"hgvs_c": "c.492+1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024303796.1",
"strand": false,
"transcript": "XM_024448028.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "TEC",
"canonical": false,
"cdna_end": null,
"cdna_length": 1728,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000624563.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000280401",
"hgvs_c": "n.457C>T",
"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": "ENST00000624563.1",
"transcript_support_level": 6
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999990361384395,
"dbsnp": "rs878855044",
"effect": "splice_donor_variant,intron_variant",
"frequency_reference_population": 0.0000065700433,
"gene_hgnc_id": 7865,
"gene_symbol": "NODAL",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657004,
"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": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Heterotaxy, visceral, 5, autosomal|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.508,
"pos": 70435285,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9340000152587891,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.99,
"transcript": "NM_018055.5"
}
]
}