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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: 18-43274323-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=43274323&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SYT4",
"hgnc_id": 11512,
"hgvs_c": "c.106A>C",
"hgvs_p": "p.Ile36Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_020783.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.166,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"chr": "18",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.45166265964508057,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 425,
"aa_ref": "I",
"aa_start": 36,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3936,
"cdna_start": 315,
"cds_end": null,
"cds_length": 1278,
"cds_start": 106,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_020783.4",
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"hgvs_c": "c.106A>C",
"hgvs_p": "p.Ile36Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000255224.8",
"protein_coding": true,
"protein_id": "NP_065834.1",
"strand": false,
"transcript": "NM_020783.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 425,
"aa_ref": "I",
"aa_start": 36,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3936,
"cdna_start": 315,
"cds_end": null,
"cds_length": 1278,
"cds_start": 106,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000255224.8",
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"hgvs_c": "c.106A>C",
"hgvs_p": "p.Ile36Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020783.4",
"protein_coding": true,
"protein_id": "ENSP00000255224.2",
"strand": false,
"transcript": "ENST00000255224.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 746,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000585604.1",
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"hgvs_c": "n.158-2491A>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000585604.1",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 424,
"aa_ref": "I",
"aa_start": 36,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3828,
"cdna_start": 212,
"cds_end": null,
"cds_length": 1275,
"cds_start": 106,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000967898.1",
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"hgvs_c": "c.106A>C",
"hgvs_p": "p.Ile36Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637957.1",
"strand": false,
"transcript": "ENST00000967898.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 407,
"aa_ref": "I",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1765,
"cdna_start": 261,
"cds_end": null,
"cds_length": 1224,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000590752.5",
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"hgvs_c": "c.52A>C",
"hgvs_p": "p.Ile18Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466930.1",
"strand": false,
"transcript": "ENST00000590752.5",
"transcript_support_level": 2
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 142,
"aa_ref": "G",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 560,
"cdna_start": 201,
"cds_end": null,
"cds_length": 431,
"cds_start": 72,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000593720.1",
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"hgvs_c": "c.72A>C",
"hgvs_p": "p.Gly24Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000472583.1",
"strand": false,
"transcript": "ENST00000593720.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 102,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 565,
"cdna_start": null,
"cds_end": null,
"cds_length": 309,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000596867.1",
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"hgvs_c": "c.-5-700A>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000470516.1",
"strand": false,
"transcript": "ENST00000596867.1",
"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": 510,
"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": "ENST00000591820.1",
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"hgvs_c": "n.220A>C",
"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": "ENST00000591820.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1142,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000586678.1",
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"hgvs_c": "n.247+2966A>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000586678.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1214631527",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 11512,
"gene_symbol": "SYT4",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.626,
"pos": 43274323,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.236,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_020783.4"
}
]
}