← 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: 13-31247967-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=31247967&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"splice_donor_variant",
"intron_variant"
],
"gene_symbol": "B3GLCT",
"hgnc_id": 20207,
"hgvs_c": "c.459+1G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_194318.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 29,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.37,
"chr": "13",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Inborn genetic diseases,Peters plus syndrome,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": 0.3700000047683716,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 498,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4215,
"cdna_start": null,
"cds_end": null,
"cds_length": 1497,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_194318.4",
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"hgvs_c": "c.459+1G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000343307.5",
"protein_coding": true,
"protein_id": "NP_919299.3",
"strand": true,
"transcript": "NM_194318.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 498,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4215,
"cdna_start": null,
"cds_end": null,
"cds_length": 1497,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000343307.5",
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"hgvs_c": "c.459+1G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_194318.4",
"protein_coding": true,
"protein_id": "ENSP00000343002.4",
"strand": true,
"transcript": "ENST00000343307.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 435,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3272,
"cdna_start": null,
"cds_end": null,
"cds_length": 1308,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000873566.1",
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"hgvs_c": "c.271-12979G>A",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543625.1",
"strand": true,
"transcript": "ENST00000873566.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 385,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1588,
"cdna_start": null,
"cds_end": null,
"cds_length": 1158,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000946543.1",
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"hgvs_c": "c.121-12979G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000616602.1",
"strand": true,
"transcript": "ENST00000946543.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 479,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4088,
"cdna_start": null,
"cds_end": null,
"cds_length": 1440,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_006719768.4",
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"hgvs_c": "c.402+1G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006719831.1",
"strand": true,
"transcript": "XM_006719768.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 458,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4095,
"cdna_start": null,
"cds_end": null,
"cds_length": 1377,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011534936.2",
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"hgvs_c": "c.459+1G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011533238.1",
"strand": true,
"transcript": "XM_011534936.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 449,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4054,
"cdna_start": null,
"cds_end": null,
"cds_length": 1350,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011534938.3",
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"hgvs_c": "c.312+1G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011533240.1",
"strand": true,
"transcript": "XM_011534938.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 449,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4061,
"cdna_start": null,
"cds_end": null,
"cds_length": 1350,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047430110.1",
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"hgvs_c": "c.312+1G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286066.1",
"strand": true,
"transcript": "XM_047430110.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 298,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1135,
"cdna_start": null,
"cds_end": null,
"cds_length": 897,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047430111.1",
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"hgvs_c": "c.459+1G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286067.1",
"strand": true,
"transcript": "XM_047430111.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999990361384395,
"dbsnp": "rs767361165",
"effect": "splice_donor_variant,intron_variant",
"frequency_reference_population": 0.00001911562,
"gene_hgnc_id": 20207,
"gene_symbol": "B3GLCT",
"gnomad_exomes_ac": 28,
"gnomad_exomes_af": 0.0000205135,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065735,
"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": "Peters plus syndrome|not provided|Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.626,
"pos": 31247967,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9359999895095825,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.93,
"transcript": "NM_194318.4"
}
]
}