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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: 13-76992279-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=76992279&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"splice_region_variant",
"intron_variant"
],
"gene_symbol": "CLN5",
"hgnc_id": 2076,
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_006493.4",
"verdict": "Benign"
},
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"splice_region_variant",
"intron_variant"
],
"gene_symbol": "ENSG00000283208",
"hgnc_id": null,
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -20,
"transcript": "ENST00000638147.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_score": -20,
"allele_count_reference_population": 61812,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.69,
"chr": "13",
"clinvar_classification": "Benign",
"clinvar_disease": " Dominant/Recessive,Neuronal Ceroid-Lipofuscinosis,Neuronal ceroid lipofuscinosis,Neuronal ceroid lipofuscinosis 5,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:9",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6899999976158142,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 358,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5243,
"cdna_start": null,
"cds_end": null,
"cds_length": 1077,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_006493.4",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000377453.9",
"protein_coding": true,
"protein_id": "NP_006484.2",
"strand": true,
"transcript": "NM_006493.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 358,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5243,
"cdna_start": null,
"cds_end": null,
"cds_length": 1077,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000377453.9",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006493.4",
"protein_coding": true,
"protein_id": "ENSP00000366673.5",
"strand": true,
"transcript": "ENST00000377453.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 358,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6664,
"cdna_start": null,
"cds_end": null,
"cds_length": 1077,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000636183.2",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490181.2",
"strand": true,
"transcript": "ENST00000636183.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 201,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1863,
"cdna_start": null,
"cds_end": null,
"cds_length": 606,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000638147.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000283208",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490953.2",
"strand": true,
"transcript": "ENST00000638147.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 273,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5060,
"cdna_start": null,
"cds_end": null,
"cds_length": 822,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000637397.2",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490422.2",
"strand": true,
"transcript": "ENST00000637397.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 270,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2508,
"cdna_start": null,
"cds_end": null,
"cds_length": 813,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000636525.2",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490078.2",
"strand": true,
"transcript": "ENST00000636525.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 248,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2368,
"cdna_start": null,
"cds_end": null,
"cds_length": 747,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000636767.2",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489855.2",
"strand": true,
"transcript": "ENST00000636767.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 207,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2527,
"cdna_start": null,
"cds_end": null,
"cds_length": 624,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000616833.6",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000479547.3",
"strand": true,
"transcript": "ENST00000616833.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 197,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5286,
"cdna_start": null,
"cds_end": null,
"cds_length": 594,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001366624.2",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001353553.1",
"strand": true,
"transcript": "NM_001366624.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 197,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2683,
"cdna_start": null,
"cds_end": null,
"cds_length": 594,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000636780.2",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489809.2",
"strand": true,
"transcript": "ENST00000636780.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 197,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2520,
"cdna_start": null,
"cds_end": null,
"cds_length": 594,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000637537.2",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489711.2",
"strand": true,
"transcript": "ENST00000637537.2",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 191,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2341,
"cdna_start": null,
"cds_end": null,
"cds_length": 576,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000485938.4",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "c.173+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000482959.3",
"strand": true,
"transcript": "ENST00000485938.4",
"transcript_support_level": 2
},
{
"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": 2791,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000635905.1",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "n.174+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000635905.1",
"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": 2517,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000635915.1",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "n.110+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490560.1",
"strand": true,
"transcript": "ENST00000635915.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 604,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000635989.1",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "n.183+8C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000635989.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2511,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000636405.1",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "n.-78C>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": "ENST00000636405.1",
"transcript_support_level": 6
},
{
"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": 1791,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000636681.1",
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"hgvs_c": "n.-656C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000489922.1",
"strand": true,
"transcript": "ENST00000636681.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.0000454702603989353,
"dbsnp": "rs9565308",
"effect": "splice_region_variant,intron_variant",
"frequency_reference_population": 0.042991158,
"gene_hgnc_id": 2076,
"gene_symbol": "CLN5",
"gnomad_exomes_ac": 56000,
"gnomad_exomes_af": 0.0434571,
"gnomad_exomes_homalt": 1613,
"gnomad_genomes_ac": 5812,
"gnomad_genomes_af": 0.0389654,
"gnomad_genomes_homalt": 221,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1834,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Neuronal Ceroid-Lipofuscinosis, Dominant/Recessive|not provided|Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.562,
"pos": 76992279,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.0020000000949949026,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006493.4"
}
]
}