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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: 10-133557078-CTGTT-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=133557078&ref=CTGTT&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PP5_Moderate"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "SYCE1",
"hgnc_id": 28852,
"hgvs_c": "c.449_452delAACA",
"hgvs_p": "p.Lys150fs",
"inheritance_mode": "AR,AD",
"pathogenic_score": 10,
"score": 10,
"transcript": "NM_001143764.3",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP5_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "CYP2E1",
"hgnc_id": 2631,
"hgvs_c": "n.3781_3784delTGTT",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "ENST00000368520.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Moderate",
"acmg_score": 10,
"allele_count_reference_population": 54,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "10",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 351,
"aa_ref": "KQ",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1255,
"cdna_start": 506,
"cds_end": null,
"cds_length": 1056,
"cds_start": 449,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001143764.3",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.449_452delAACA",
"hgvs_p": "p.Lys150fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000343131.7",
"protein_coding": true,
"protein_id": "NP_001137236.1",
"strand": false,
"transcript": "NM_001143764.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 351,
"aa_ref": "KQ",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1255,
"cdna_start": 506,
"cds_end": null,
"cds_length": 1056,
"cds_start": 449,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000343131.7",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.449_452delAACA",
"hgvs_p": "p.Lys150fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001143764.3",
"protein_coding": true,
"protein_id": "ENSP00000341282.5",
"strand": false,
"transcript": "ENST00000343131.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 318,
"aa_ref": "KQ",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1011,
"cdna_start": 506,
"cds_end": null,
"cds_length": 957,
"cds_start": 449,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000303903.10",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.449_452delAACA",
"hgvs_p": "p.Lys150fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000303978.5",
"strand": false,
"transcript": "ENST00000303903.10",
"transcript_support_level": 1
},
{
"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": 7918,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000368520.1",
"gene_hgnc_id": 2631,
"gene_symbol": "CYP2E1",
"hgvs_c": "n.3781_3784delTGTT",
"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": "ENST00000368520.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 384,
"aa_ref": "KQ",
"aa_start": 183,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1317,
"cdna_start": 570,
"cds_end": null,
"cds_length": 1155,
"cds_start": 548,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000863039.1",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.548_551delAACA",
"hgvs_p": "p.Lys183fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533098.1",
"strand": false,
"transcript": "ENST00000863039.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 352,
"aa_ref": "KQ",
"aa_start": 151,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1239,
"cdna_start": 485,
"cds_end": null,
"cds_length": 1059,
"cds_start": 452,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000863036.1",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.452_455delAACA",
"hgvs_p": "p.Lys151fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533095.1",
"strand": false,
"transcript": "ENST00000863036.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 330,
"aa_ref": "KQ",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1158,
"cdna_start": 405,
"cds_end": null,
"cds_length": 993,
"cds_start": 386,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000863038.1",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.386_389delAACA",
"hgvs_p": "p.Lys129fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533097.1",
"strand": false,
"transcript": "ENST00000863038.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 318,
"aa_ref": "KQ",
"aa_start": 150,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1402,
"cdna_start": 506,
"cds_end": null,
"cds_length": 957,
"cds_start": 449,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001143763.2",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.449_452delAACA",
"hgvs_p": "p.Lys150fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001137235.1",
"strand": false,
"transcript": "NM_001143763.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 282,
"aa_ref": "KQ",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1379,
"cdna_start": 483,
"cds_end": null,
"cds_length": 849,
"cds_start": 341,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_130784.4",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.341_344delAACA",
"hgvs_p": "p.Lys114fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_570140.1",
"strand": false,
"transcript": "NM_130784.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 282,
"aa_ref": "KQ",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1377,
"cdna_start": 483,
"cds_end": null,
"cds_length": 849,
"cds_start": 341,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000368517.7",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.341_344delAACA",
"hgvs_p": "p.Lys114fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000357503.3",
"strand": false,
"transcript": "ENST00000368517.7",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 322,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1165,
"cdna_start": null,
"cds_end": null,
"cds_length": 969,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000863035.1",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.378-260_378-257delAACA",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533094.1",
"strand": false,
"transcript": "ENST00000863035.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 321,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1141,
"cdna_start": null,
"cds_end": null,
"cds_length": 966,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000863037.1",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "c.375-260_375-257delAACA",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533096.1",
"strand": false,
"transcript": "ENST00000863037.1",
"transcript_support_level": null
},
{
"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": 2479,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000479535.2",
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"hgvs_c": "n.1582_1585delAACA",
"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": "ENST00000479535.2",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs779142116",
"effect": "frameshift_variant",
"frequency_reference_population": 0.000033456836,
"gene_hgnc_id": 28852,
"gene_symbol": "SYCE1",
"gnomad_exomes_ac": 49,
"gnomad_exomes_af": 0.0000335197,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328532,
"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": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.038,
"pos": 133557078,
"ref": "CTGTT",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.029999999329447746,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_001143764.3"
}
]
}