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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: 11-17779570-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=17779570&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "KCNC1",
"hgnc_id": 6233,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Arg540His",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001112741.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BP6,BS2",
"acmg_score": -6,
"allele_count_reference_population": 49,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1154,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.09,
"chr": "11",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Inborn genetic diseases,Progressive myoclonic epilepsy type 7,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.3649342656135559,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 585,
"aa_ref": "R",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4303,
"cdna_start": 2841,
"cds_end": null,
"cds_length": 1758,
"cds_start": 1619,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001112741.2",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Arg540His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000265969.8",
"protein_coding": true,
"protein_id": "NP_001106212.1",
"strand": true,
"transcript": "NM_001112741.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 585,
"aa_ref": "R",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4303,
"cdna_start": 2841,
"cds_end": null,
"cds_length": 1758,
"cds_start": 1619,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000265969.8",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Arg540His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001112741.2",
"protein_coding": true,
"protein_id": "ENSP00000265969.7",
"strand": true,
"transcript": "ENST00000265969.8",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 625,
"aa_ref": "R",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4329,
"cdna_start": 2841,
"cds_end": null,
"cds_length": 1878,
"cds_start": 1619,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000639325.2",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Arg540His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492663.2",
"strand": true,
"transcript": "ENST00000639325.2",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 625,
"aa_ref": "R",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4322,
"cdna_start": 2841,
"cds_end": null,
"cds_length": 1878,
"cds_start": 1619,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000640318.2",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Arg540His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000491189.2",
"strand": true,
"transcript": "ENST00000640318.2",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 566,
"aa_ref": "R",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3468,
"cdna_start": 2841,
"cds_end": null,
"cds_length": 1701,
"cds_start": 1619,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000675775.1",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Arg540His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502716.1",
"strand": true,
"transcript": "ENST00000675775.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 78,
"aa_ref": "R",
"aa_start": 52,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3102,
"cdna_start": 156,
"cds_end": null,
"cds_length": 237,
"cds_start": 155,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000638825.1",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "c.155G>A",
"hgvs_p": "p.Arg52His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000491247.1",
"strand": true,
"transcript": "ENST00000638825.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 181,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2530,
"cdna_start": null,
"cds_end": null,
"cds_length": 546,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000639495.1",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "c.406+6972G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000491700.1",
"strand": true,
"transcript": "ENST00000639495.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 69,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 537,
"cdna_start": null,
"cds_end": null,
"cds_length": 210,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000640461.1",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "c.70+6972G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000491345.1",
"strand": true,
"transcript": "ENST00000640461.1",
"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": 525,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000525802.1",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "n.395G>A",
"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": "ENST00000525802.1",
"transcript_support_level": 4
},
{
"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": 1859,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000526029.1",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "n.399G>A",
"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": "ENST00000526029.1",
"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": 660,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000638366.1",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "n.*103G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000491016.1",
"strand": true,
"transcript": "ENST00000638366.1",
"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": 849,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000638395.1",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "n.320G>A",
"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": "ENST00000638395.1",
"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": 3335,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000640909.2",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "n.1619G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000491644.2",
"strand": true,
"transcript": "ENST00000640909.2",
"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": 660,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000638366.1",
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"hgvs_c": "n.*103G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000491016.1",
"strand": true,
"transcript": "ENST00000638366.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs375362627",
"effect": "missense_variant",
"frequency_reference_population": 0.00003158352,
"gene_hgnc_id": 6233,
"gene_symbol": "KCNC1",
"gnomad_exomes_ac": 45,
"gnomad_exomes_af": 0.0000321603,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262809,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Progressive myoclonic epilepsy type 7|Inborn genetic diseases|not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.73,
"pos": 17779570,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.745,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001112741.2"
}
]
}