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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: 1-40097210-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40097210&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PS3",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "PPT1",
"hgnc_id": 9325,
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"inheritance_mode": "AR",
"pathogenic_score": 20,
"score": 20,
"transcript": "NM_000310.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PS3,PP5_Very_Strong",
"acmg_score": 20,
"allele_count_reference_population": 144,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.28,
"chr": "1",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Inborn genetic diseases,Neuronal ceroid lipofuscinosis,Neuronal ceroid lipofuscinosis 1,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.2800000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 306,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2284,
"cdna_start": 43,
"cds_end": null,
"cds_length": 921,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_000310.4",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000642050.2",
"protein_coding": true,
"protein_id": "NP_000301.1",
"strand": false,
"transcript": "NM_000310.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 306,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2284,
"cdna_start": 43,
"cds_end": null,
"cds_length": 921,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000642050.2",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000310.4",
"protein_coding": true,
"protein_id": "ENSP00000493153.1",
"strand": false,
"transcript": "ENST00000642050.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 305,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2267,
"cdna_start": 43,
"cds_end": null,
"cds_length": 918,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000433473.8",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000394863.4",
"strand": false,
"transcript": "ENST00000433473.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2340,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000530704.6",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "n.29T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000431655.1",
"strand": false,
"transcript": "ENST00000530704.6",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 335,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2368,
"cdna_start": 38,
"cds_end": null,
"cds_length": 1008,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000641471.1",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493146.1",
"strand": false,
"transcript": "ENST00000641471.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 322,
"aa_ref": "L",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2353,
"cdna_start": 7,
"cds_end": null,
"cds_length": 969,
"cds_start": 5,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000641083.1",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.5T>A",
"hgvs_p": "p.Leu2*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493369.1",
"strand": false,
"transcript": "ENST00000641083.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 311,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2314,
"cdna_start": 58,
"cds_end": null,
"cds_length": 936,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000917762.1",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587821.1",
"strand": false,
"transcript": "ENST00000917762.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 301,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2388,
"cdna_start": 45,
"cds_end": null,
"cds_length": 906,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000641319.1",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493128.1",
"strand": false,
"transcript": "ENST00000641319.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 282,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3463,
"cdna_start": 43,
"cds_end": null,
"cds_length": 849,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001363695.2",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001350624.1",
"strand": false,
"transcript": "NM_001363695.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 282,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2195,
"cdna_start": 43,
"cds_end": null,
"cds_length": 849,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000439754.6",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403207.2",
"strand": false,
"transcript": "ENST00000439754.6",
"transcript_support_level": 3
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 207,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 638,
"cdna_start": 43,
"cds_end": null,
"cds_length": 624,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000527311.7",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000436695.3",
"strand": false,
"transcript": "ENST00000527311.7",
"transcript_support_level": 3
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 203,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3226,
"cdna_start": 43,
"cds_end": null,
"cds_length": 612,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001142604.2",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001136076.1",
"strand": false,
"transcript": "NM_001142604.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 203,
"aa_ref": "L",
"aa_start": 10,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1957,
"cdna_start": 51,
"cds_end": null,
"cds_length": 612,
"cds_start": 29,
"consequences": [
"stop_gained"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000449045.7",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "c.29T>A",
"hgvs_p": "p.Leu10*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000392293.2",
"strand": false,
"transcript": "ENST00000449045.7",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 588,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000372779.9",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "n.29T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000361865.5",
"strand": false,
"transcript": "ENST00000372779.9",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 731,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000526547.2",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "n.2T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000436481.2",
"strand": false,
"transcript": "ENST00000526547.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1836,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000529905.5",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "n.29T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000432053.1",
"strand": false,
"transcript": "ENST00000529905.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2481,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000641236.1",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "n.41T>A",
"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": "ENST00000641236.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 507,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000641548.1",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "n.29T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000492984.1",
"strand": false,
"transcript": "ENST00000641548.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2253,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000641691.1",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "n.29T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000492910.1",
"strand": false,
"transcript": "ENST00000641691.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 550,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000641924.1",
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"hgvs_c": "n.29T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000493063.1",
"strand": false,
"transcript": "ENST00000641924.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs137852699",
"effect": "stop_gained",
"frequency_reference_population": 0.000089225854,
"gene_hgnc_id": 9325,
"gene_symbol": "PPT1",
"gnomad_exomes_ac": 138,
"gnomad_exomes_af": 0.0000944104,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 6,
"gnomad_genomes_af": 0.0000394275,
"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",
"phenotype_combined": "Neuronal ceroid lipofuscinosis 1|not provided|Neuronal ceroid lipofuscinosis|Inborn genetic diseases",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.354,
"pos": 40097210,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000310.4"
}
]
}