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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: 1-40080393-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40080393&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 40080393,
"ref": "T",
"alt": "C",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000642050.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.627+4A>G",
"hgvs_p": null,
"transcript": "NM_000310.4",
"protein_id": "NP_000301.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 306,
"cds_start": -4,
"cds_end": null,
"cds_length": 921,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2284,
"mane_select": "ENST00000642050.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.627+4A>G",
"hgvs_p": null,
"transcript": "ENST00000642050.2",
"protein_id": "ENSP00000493153.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 306,
"cds_start": -4,
"cds_end": null,
"cds_length": 921,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2284,
"mane_select": "NM_000310.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.624+4A>G",
"hgvs_p": null,
"transcript": "ENST00000433473.8",
"protein_id": "ENSP00000394863.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 305,
"cds_start": -4,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*250+4A>G",
"hgvs_p": null,
"transcript": "ENST00000530704.6",
"protein_id": "ENSP00000431655.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2340,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.714+4A>G",
"hgvs_p": null,
"transcript": "ENST00000641471.1",
"protein_id": "ENSP00000493146.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 335,
"cds_start": -4,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2368,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.603+4A>G",
"hgvs_p": null,
"transcript": "ENST00000641083.1",
"protein_id": "ENSP00000493369.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 322,
"cds_start": -4,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2353,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.627+4A>G",
"hgvs_p": null,
"transcript": "ENST00000641319.1",
"protein_id": "ENSP00000493128.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 301,
"cds_start": -4,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.627+4A>G",
"hgvs_p": null,
"transcript": "NM_001363695.2",
"protein_id": "NP_001350624.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 282,
"cds_start": -4,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.627+4A>G",
"hgvs_p": null,
"transcript": "ENST00000439754.6",
"protein_id": "ENSP00000403207.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 282,
"cds_start": -4,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.396+4A>G",
"hgvs_p": null,
"transcript": "ENST00000527311.7",
"protein_id": "ENSP00000436695.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 207,
"cds_start": -4,
"cds_end": null,
"cds_length": 624,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.318+4A>G",
"hgvs_p": null,
"transcript": "NM_001142604.2",
"protein_id": "NP_001136076.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 203,
"cds_start": -4,
"cds_end": null,
"cds_length": 612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.318+4A>G",
"hgvs_p": null,
"transcript": "ENST00000449045.7",
"protein_id": "ENSP00000392293.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 203,
"cds_start": -4,
"cds_end": null,
"cds_length": 612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1957,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.-31+4A>G",
"hgvs_p": null,
"transcript": "ENST00000530076.6",
"protein_id": "ENSP00000434007.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 87,
"cds_start": -4,
"cds_end": null,
"cds_length": 264,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.147-3480A>G",
"hgvs_p": null,
"transcript": "ENST00000641381.1",
"protein_id": "ENSP00000493359.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 77,
"cds_start": -4,
"cds_end": null,
"cds_length": 234,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.627+4A>G",
"hgvs_p": null,
"transcript": "ENST00000529905.5",
"protein_id": "ENSP00000432053.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.864+4A>G",
"hgvs_p": null,
"transcript": "ENST00000641236.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*479+4A>G",
"hgvs_p": null,
"transcript": "ENST00000641691.1",
"protein_id": "ENSP00000492910.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*56+4A>G",
"hgvs_p": null,
"transcript": "ENST00000641924.1",
"protein_id": "ENSP00000493063.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*467A>G",
"hgvs_p": null,
"transcript": "ENST00000372779.9",
"protein_id": "ENSP00000361865.5",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"dbsnp": "rs572153728",
"frequency_reference_population": 0.0007814514,
"hom_count_reference_population": 13,
"allele_count_reference_population": 1261,
"gnomad_exomes_af": 0.000813621,
"gnomad_genomes_af": 0.000472764,
"gnomad_exomes_ac": 1189,
"gnomad_genomes_ac": 72,
"gnomad_exomes_homalt": 13,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.27000001072883606,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.6880000233650208,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.044,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.12,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.94492105287782,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -18,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000642050.2",
"gene_symbol": "PPT1",
"hgnc_id": 9325,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.627+4A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Neuronal ceroid lipofuscinosis 1,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"phenotype_combined": "not specified|not provided|Neuronal ceroid lipofuscinosis 1|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}